├── .gitignore ├── Analysis ├── Scripts │ ├── dcd_loader_script.vmd │ ├── setup_representations.vmd │ ├── total_loader.vmd │ ├── volmap_generator.vmd │ ├── volmap_generator_ions.vmd │ └── volmap_generator_water.vmd ├── analysis_mdtraj.py ├── dcd_trajectory_fileloader.vmd ├── generic_loader.vmd ├── job_reminder.sh ├── model_loader.vmd └── sort.sh ├── BUILD_DIR ├── AminoAcids │ ├── ala.pdb │ ├── arg.pdb │ ├── asn.pdb │ ├── asp.pdb │ ├── cys.pdb │ ├── gln.pdb │ ├── glu.pdb │ ├── gly.pdb │ ├── his.pdb │ ├── ile.pdb │ ├── leu.pdb │ ├── lys.pdb │ ├── met.pdb │ ├── phe.pdb │ ├── pro.pdb │ ├── ser.pdb │ ├── thr.pdb │ ├── trp.pdb │ ├── tyr.pdb │ └── val.pdb ├── ProcessScript_example.sh ├── SmallMolecules │ ├── 2propanol.pdb │ ├── 3phosglycer.pdb │ ├── 6phosgluc.pdb │ ├── ATP.mol2 │ ├── ATP.pdb │ ├── ATP2.mol2 │ ├── CTP.pdb │ ├── GSH.pdb │ ├── GTP.pdb │ ├── Mol2 │ │ ├── 3phosglycerate.mol2 │ │ ├── 6phosgluc.mol2 │ │ ├── CTP.mol2 │ │ ├── GTP.mol2 │ │ ├── UDP.mol2 │ │ ├── UDP_GlcNAc.mol2 │ │ ├── UDPglucose.mol2 │ │ ├── UTP.mol2 │ │ ├── alanine.mol2 │ │ ├── aspartate.mol2 │ │ ├── citrate.mol2 │ │ ├── citrulline.mol2 │ │ ├── coenzymeA.mol2 │ │ ├── dTTP.mol2 │ │ ├── fructose_1_6_biphosphate.mol2 │ │ ├── glutamate.mol2 │ │ ├── glutamine.mol2 │ │ ├── glutathione.mol2 │ │ ├── glutdisul.mol2 │ │ ├── glycerate.mol2 │ │ ├── hexoseP.mol2 │ │ ├── malate.mol2 │ │ ├── nad.mol2 │ │ ├── uridine.mol2 │ │ └── valine.mol2 │ ├── OLDPDB │ │ └── atp.pdb │ ├── UDP.pdb │ ├── UDPGlcNAc.pdb │ ├── UDPglucose.pdb │ ├── UTP.pdb │ ├── acetamide.pdb │ ├── alanine.pdb │ ├── aspartate.pdb │ ├── b_galactose.pdb │ ├── b_glucose.pdb │ ├── benzene.pdb │ ├── benzoate.pdb │ ├── butane.pdb │ ├── citrate.pdb │ ├── citrulline.pdb │ ├── coenzymeA.pdb │ ├── coumarin.pdb │ ├── dTTP.pdb │ ├── ethanol.pdb │ ├── fruct16biphos.pdb │ ├── fructose_1_6_biphosphate.pdb │ ├── galactose.pdb │ ├── glutamate.pdb │ ├── glutamine.pdb │ ├── glutathione.mol2.txt │ ├── glutathione.pdb │ ├── glutdisul.pdb │ ├── glycerate.pdb │ ├── hexoseP.pdb │ ├── imidazole.pdb │ ├── malate.pdb │ ├── methanol.pdb │ ├── mg_ion.pdb │ ├── mol.pdb │ ├── mol.pdb.bup │ ├── n_ben_acet.pdb │ ├── n_benzylacetamide.pdb │ ├── n_methyl_acetamide.pdb │ ├── nad.pdb │ ├── nadph.pdb │ ├── nadph_docked.pdb │ ├── octanol.pdb │ ├── oxindol_3_ylidene_rhodanine.pdb │ ├── p_ethylphenol.pdb │ ├── phenol.pdb │ ├── phenyl_sulfamate.pdb │ ├── propionic_acid.pdb │ ├── uridine.pdb │ └── valine.pdb ├── build_example ├── build_notes.txt ├── hexagonal_solvate.vmd ├── model_temp_x.pdb ├── model_temp_x.psf ├── molecule_prep_helper1.vmd ├── optimization_01.coor ├── optimization_01.dcd ├── optimization_01.restart.coor ├── optimization_01.restart.vel ├── optimization_01.restart.xsc ├── optimization_01.vel ├── optimization_01.xsc ├── optimization_01.xst ├── packmol ├── packmol_config_file.cfg ├── rhombicdodecahedron.tcl ├── sim_model_prep.conf ├── sim_opt.conf ├── solvate_ionize_script.vmd └── stride_workaround_2019.tcl ├── Examples ├── 1ubq_chainA.pdb ├── create_local_dcd_loader_script ├── master_config_file └── readme.txt ├── InputFiles ├── Parameters │ ├── 00toppar_file_format.txt │ ├── 3phosglycerate.str │ ├── 6phosgluc.str │ ├── CTP.str │ ├── GTP.str │ ├── UDP.str │ ├── UDP_GlcNAc.str │ ├── UDPglucose.str │ ├── UTP.str │ ├── ace │ │ ├── acepar19.inp │ │ ├── acepar22_prot.inp │ │ └── acepar27_na.inp │ ├── alanine.str │ ├── aspartate.str │ ├── atp.str │ ├── cheq │ │ ├── par_all30_cheq_prot.inp │ │ └── top_all30_cheq_prot.inp │ ├── citrate.str │ ├── citrulline.str │ ├── coenzymeA.str │ ├── dTTP.str │ ├── drude │ │ ├── 00readme_2019_release.txt │ │ ├── drude_toppar_2019.tgz │ │ ├── positive_drude.tgz │ │ ├── toppar_defs_2019.str │ │ ├── toppar_drude_carbohydrate_2019a.str │ │ ├── toppar_drude_d_aminoacids_2019g.str │ │ ├── toppar_drude_lipid_2017c.str │ │ ├── toppar_drude_master_protein_2019g.str │ │ ├── toppar_drude_model_2019g.str │ │ └── toppar_drude_nucleic_acid_2017c.str │ ├── fruct16biphos.str │ ├── fructose_1_6_biphosphate.str │ ├── gbsw │ │ ├── 00readme │ │ ├── par_all22_prot_gbsw.inp │ │ ├── radii_prot_na.str │ │ └── radius_gbsw.str │ ├── glutamate.str │ ├── glutamine.str │ ├── glutathione.str │ ├── glutdisulf.str │ ├── glycerate.str │ ├── hexoseP.str │ ├── larmord │ │ └── larmord_rna.dat │ ├── malate.str │ ├── metabolites_2018.str │ ├── metabolites_2018_par.str │ ├── metals │ │ └── CHARMM_METAL.tgz │ ├── nad.str │ ├── non_charmm │ │ ├── 00readme │ │ ├── gromacs │ │ │ └── charmm36-mar2019.ff.tgz │ │ ├── par_amber_98.inp │ │ ├── par_amber_cornell.inp │ │ ├── par_bms_dec03.inp │ │ ├── par_opls_aa.inp │ │ ├── par_opls_aam.inp │ │ ├── par_opls_ligand.inp │ │ ├── parm14sb_all.prm │ │ ├── parm14sb_all.rtf │ │ ├── top_amber_cornell.inp │ │ ├── top_bms_dec03.inp │ │ ├── top_opls_aa.inp │ │ ├── top_opls_aam.inp │ │ ├── toppar_chloroform_dh.str │ │ ├── toppar_ions_nbfix_uiuc.str │ │ ├── toppar_water_ions_spc.str │ │ ├── toppar_water_ions_spc_e.str │ │ ├── toppar_water_ions_tip3p_pme_b.str │ │ ├── toppar_water_ions_tip3p_pme_f.str │ │ ├── toppar_water_ions_tip4p.str │ │ ├── toppar_water_ions_tip4p_2005.str │ │ ├── toppar_water_ions_tip4p_ew.str │ │ ├── toppar_water_ions_tip5p.str │ │ └── toppar_water_ions_tip5p_ew.str │ ├── openmm_gbsaobc2 │ │ ├── charmm_all36_na_gbsaobc.str │ │ ├── charmm_all36_prot+na_gbsaobc.str │ │ ├── charmm_all36_prot_gbsaobc.str │ │ └── makednarna_obc.pl │ ├── par_all22_prot.prm │ ├── par_all35_ethers.prm │ ├── par_all36_carb.prm │ ├── par_all36_cgenff.prm │ ├── par_all36_lipid.prm │ ├── par_all36_na.prm │ ├── par_all36_prot.prm │ ├── par_all36_water_ions.prm │ ├── par_all36m_prot.prm │ ├── par_hbond.inp │ ├── param19.inp │ ├── protpatch_protein_toppar36.str │ ├── rush │ │ ├── par_rush_058.inp │ │ ├── par_rush_058_a.cmap │ │ └── top_rush_058.inp │ ├── silicates │ │ ├── 00README │ │ ├── code │ │ │ ├── cell.f │ │ │ ├── compile.txt │ │ │ ├── crystal.dat │ │ │ ├── crystal.f │ │ │ ├── input.xyz │ │ │ ├── patches.dat │ │ │ ├── patchfind.f │ │ │ └── patchfind.x │ │ ├── crystal.dat │ │ ├── crystal.img │ │ ├── image_patch.str │ │ ├── input.xyz │ │ ├── params.str │ │ ├── patches.dat │ │ ├── quartz_init.pdb │ │ ├── supp_mat_oct05.tar │ │ ├── test.inp │ │ ├── test.out │ │ ├── test_opt.crd │ │ ├── test_opt.pdb │ │ ├── test_opt.psf │ │ └── toppar │ │ │ ├── par_silicates.inp │ │ │ └── top_silicates.inp │ ├── stream │ │ ├── carb │ │ │ ├── toppar_all36_carb_glycolipid.str │ │ │ ├── toppar_all36_carb_glycopeptide.str │ │ │ ├── toppar_all36_carb_imlab.str │ │ │ ├── toppar_all36_carb_lignin.str │ │ │ └── toppar_all36_carb_model.str │ │ ├── cphmd │ │ │ └── protpatch_protein_toppar36.str │ │ ├── lipid │ │ │ ├── toppar_all36_lipid_bacterial.str │ │ │ ├── toppar_all36_lipid_cardiolipin.str │ │ │ ├── toppar_all36_lipid_cationpi_wyf.str │ │ │ ├── toppar_all36_lipid_cholesterol.str │ │ │ ├── toppar_all36_lipid_detergent.str │ │ │ ├── toppar_all36_lipid_ether.str │ │ │ ├── toppar_all36_lipid_inositol.str │ │ │ ├── toppar_all36_lipid_list.str │ │ │ ├── toppar_all36_lipid_lps.str │ │ │ ├── toppar_all36_lipid_miscellaneous.str │ │ │ ├── toppar_all36_lipid_model.str │ │ │ ├── toppar_all36_lipid_prot.str │ │ │ ├── toppar_all36_lipid_sphingo.str │ │ │ └── toppar_all36_lipid_yeast.str │ │ ├── misc │ │ │ ├── toppar_amines.str │ │ │ ├── toppar_dum_noble_gases.str │ │ │ ├── toppar_hbond.str │ │ │ └── toppar_ions_won.str │ │ ├── na │ │ │ ├── toppar_all36_na_model.str │ │ │ ├── toppar_all36_na_modifications.str │ │ │ ├── toppar_all36_na_nad_ppi.str │ │ │ ├── toppar_all36_na_reactive_rna.str │ │ │ └── toppar_all36_na_rna_modified.str │ │ └── prot │ │ │ ├── toppar_all36_prot_aldehydes.str │ │ │ ├── toppar_all36_prot_arg0.str │ │ │ ├── toppar_all36_prot_c36_d_aminoacids.str │ │ │ ├── toppar_all36_prot_c36m_d_aminoacids.str │ │ │ ├── toppar_all36_prot_fluoro_alkanes.str │ │ │ ├── toppar_all36_prot_heme.str │ │ │ ├── toppar_all36_prot_model.str │ │ │ ├── toppar_all36_prot_modify_res.str │ │ │ ├── toppar_all36_prot_na_combined.str │ │ │ ├── toppar_all36_prot_pyridines.str │ │ │ └── toppar_all36_prot_retinol.str │ ├── tamdfff │ │ ├── par_all22_prot_tadcmap.ahbb4.inp │ │ ├── par_tadmap.chi1.ahbb4.inp │ │ └── top_all22_prot_cmap.ahbb4.inp │ ├── top_all22_prot.rtf │ ├── top_all35_ethers.rtf │ ├── top_all36_carb.rtf │ ├── top_all36_cgenff.rtf │ ├── top_all36_lipid.rtf │ ├── top_all36_na.rtf │ ├── top_all36_prot.rtf │ ├── toph19.inp │ ├── toppar_all.history │ ├── toppar_all.history~ │ ├── toppar_water_ions.str │ ├── toppar_water_ions_namd.str │ ├── uridine.str │ └── valine.str ├── colvars.in ├── example.pdb ├── example.psf ├── ionized.pdb └── ionized.psf ├── LICENSE ├── Project └── MovieBox │ ├── Examples │ ├── movie_setup_01.vmd │ ├── setup_01.vmd │ ├── untitled.blend │ └── viewpoints_01.tcl │ ├── Movie │ └── movie_script_01.tcl~ │ ├── Scripts │ ├── .directory │ ├── local_render_tachyon │ ├── movie_script_example_01.tcl │ ├── old_scripts │ │ ├── .directory │ │ ├── view_change_render.tcl │ │ ├── view_change_render_cheap.tcl │ │ ├── view_change_render_povray.tcl │ │ ├── view_change_render_tachyon.tcl │ │ └── view_change_render_v_3.tcl │ ├── pbs_render_tachyon │ ├── ppmconv │ ├── view_change_render_2007.tcl │ └── view_change_render_2012_v1.tcl │ ├── making_movies_README.txt │ └── movie_script_example_01.tcl ├── README.txt ├── Setup_and_Config ├── Benchmarking │ ├── .ipynb_checkpoints │ │ └── Benchmarking_v1-checkpoint.ipynb │ ├── BENCHMARK_SETUP.json │ ├── Benchmark_setup.py │ ├── Benchmarking_v1.ipynb │ ├── HOW_TO_RUN_BENCHMARKS.readme │ ├── Templates │ │ ├── bm_data_processing.py │ │ ├── generic_benchmark.conf │ │ ├── namd_equilibration_script.template │ │ ├── sbatch_benchmark_template │ │ └── sbatch_initial_benchmark.template │ ├── generic_benchmark.conf │ ├── raw_benchmark_data.txt │ └── run_my_benchmarks.py ├── JobTemplate │ ├── Errors │ │ └── .gitignore │ ├── JobLog │ │ └── .gitignore │ ├── LastRestart │ │ └── .gitignore │ ├── OutputFiles │ │ └── .gitignore │ ├── OutputText │ │ └── .gitignore │ └── RestartFiles │ │ └── .gitignore ├── MolecularSoup │ ├── namd_equilibration_script.conf │ ├── namd_production_script.conf │ ├── sbatch_production_script.template │ ├── sbatch_production_script.template.mpi │ └── sbatch_start_script.template ├── job_details_template.json ├── local_job_details_template.json ├── namd_equilibration_script.conf ├── namd_production_script.conf ├── postjob_processing.py ├── prejob_processing.py ├── readme.txt ├── sbatch_production_script.template ├── sbatch_production_script.template.mpi └── sbatch_start_script.template ├── function_files.txt ├── master_config_file ├── mdwf ├── mdwf_lib ├── .gitignore ├── AvocaLegacyCode │ ├── master_config_file │ ├── mdwf │ └── mdwf_functions.py ├── __init__.py ├── __init__.pyc ├── mdwf_functions.py ├── mdwf_functions.py.bak ├── mdwf_functions.py.orig └── readme.txt ├── project_plan.txt └── sbatch_backup_script /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *.pyc 5 | 6 | # Specific to MD_workflow 7 | Main_Job_Dir/* 8 | MainJobdir1/* 9 | 10 | # C extensions 11 | *.so 12 | 13 | # Distribution / packaging 14 | .Python 15 | env/ 16 | bin/ 17 | build/ 18 | develop-eggs/ 19 | dist/ 20 | eggs/ 21 | lib/ 22 | lib64/ 23 | parts/ 24 | sdist/ 25 | var/ 26 | *.egg-info/ 27 | .installed.cfg 28 | *.egg 29 | 30 | # Installer logs 31 | pip-log.txt 32 | pip-delete-this-directory.txt 33 | 34 | # Unit test / coverage reports 35 | htmlcov/ 36 | .tox/ 37 | .coverage 38 | .cache 39 | nosetests.xml 40 | coverage.xml 41 | 42 | # Translations 43 | *.mo 44 | 45 | # Mr Developer 46 | .mr.developer.cfg 47 | .project 48 | .pydevproject 49 | 50 | # Rope 51 | .ropeproject 52 | 53 | # Django stuff: 54 | *.log 55 | *.pot 56 | 57 | # Sphinx documentation 58 | docs/_build/ 59 | 60 | # Vim temporary/swap files. 61 | .*.swp 62 | .*.swo 63 | -------------------------------------------------------------------------------- /Analysis/Scripts/dcd_loader_script.vmd: -------------------------------------------------------------------------------- 1 | # DCD loader script 2 | # Script to load in the latest dcd files 'dcd_trajectory_fileloader' 3 | # This will only work if each model has a different number of atoms. 4 | # If two models have the same number of atoms trajectory files will be corrupted! 5 | # 6 | # 7 | 8 | # Expecting models to be already loaded into vmd 9 | 10 | # count models loaded: 11 | set models [molinfo num] 12 | 13 | for {set molno 0} {$molno < $models} {incr molno} { 14 | 15 | set mol_id [molinfo index $molno] 16 | mol top $mol_id 17 | source dcd_trajectory_fileloader.vmd 18 | } 19 | 20 | 21 | 22 | 23 | -------------------------------------------------------------------------------- /Analysis/Scripts/setup_representations.vmd: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/vmd 2 | # Save your representations to this file. 3 | -------------------------------------------------------------------------------- /Analysis/Scripts/total_loader.vmd: -------------------------------------------------------------------------------- 1 | # Total loader script. 2 | # simple loader script to read in models, dcd files and then perform protein alignment 3 | 4 | source setup_representations.vmd 5 | 6 | source dcd_loader_script.vmd 7 | 8 | source align_protein_backbones.vmd 9 | 10 | source volmap_generator.vmd 11 | 12 | source volmap_generator_water.vmd 13 | source volmap_generator_ions.vmd 14 | -------------------------------------------------------------------------------- /Analysis/Scripts/volmap_generator.vmd: -------------------------------------------------------------------------------- 1 | # volmap generator. 2 | # script to automatically generate occupancy maps to help determine fractional 3 | # occupancy. 4 | 5 | mol top 0 6 | 7 | set models [molinfo num] 8 | 9 | 10 | for {set molno 0} {$molno < $models} {incr molno} { 11 | 12 | set mol_id [molinfo index $molno] 13 | mol top $mol_id 14 | 15 | set frames [molinfo $mol_id get numframes] 16 | volmap occupancy [atomselect top {chain L and not hydrogen}] \ 17 | -res 1.0 -allframes -combine avg -mol top 18 | 19 | } 20 | -------------------------------------------------------------------------------- /Analysis/Scripts/volmap_generator_ions.vmd: -------------------------------------------------------------------------------- 1 | # volmap generator. 2 | # script to automatically generate occupancy maps to help determine fractional 3 | # occupancy. 4 | 5 | mol top 0 6 | 7 | set models [molinfo num] 8 | 9 | 10 | for {set molno 0} {$molno < $models} {incr molno} { 11 | 12 | set mol_id [molinfo index $molno] 13 | mol top $mol_id 14 | 15 | # generate cation set 16 | set frames [molinfo $mol_id get numframes] 17 | volmap occupancy [atomselect top {name LIT SOD MG POT CAL RUB CES BAR CAD}] \ 18 | -res 1.0 -allframes -combine avg -mol top 19 | 20 | # generate anion set 21 | set frames [molinfo $mol_id get numframes] 22 | volmap occupancy [atomselect top {name CLA}] \ 23 | -res 1.0 -allframes -combine avg -mol top 24 | } 25 | -------------------------------------------------------------------------------- /Analysis/Scripts/volmap_generator_water.vmd: -------------------------------------------------------------------------------- 1 | # volmap generator. 2 | # script to automatically generate occupancy maps to help determine fractional 3 | # occupancy. 4 | 5 | mol top 0 6 | 7 | set models [molinfo num] 8 | 9 | 10 | for {set molno 0} {$molno < $models} {incr molno} { 11 | 12 | set mol_id [molinfo index $molno] 13 | mol top $mol_id 14 | 15 | set frames [molinfo $mol_id get numframes] 16 | volmap occupancy [atomselect top {water}] \ 17 | -res 1.0 -allframes -combine avg -mol top 18 | 19 | } 20 | -------------------------------------------------------------------------------- /Analysis/generic_loader.vmd: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/vmd 2 | # VMD script written by save_state $Revision: 1.47 $ 3 | # VMD version: 1.9.3 4 | 5 | 6 | set mol_list { e2d2_aq e2d2_aq_cu1 e2d2_aq_dis e2d2_aq_21S e2d2_aq_107S e2d2_aq_111S e2d2_cu_ubq } 7 | set c 0 8 | 9 | foreach i $mol_list { 10 | 11 | mol new ../InputFiles/$i.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 12 | mol addfile ../InputFiles/$i.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 13 | 14 | mol showrep top 0 off 15 | mol representation NewCartoon 0.60 10.0 3.0 0 16 | mol color ColorID $c 17 | mol material AOChalky 18 | mol addrep top 19 | 20 | mol representation Licorice 0.4 12.0 12.0 21 | mol selection {resid 107 111 and not hydrogen and chain A} 22 | mol color Type 23 | mol addrep top 24 | 25 | mol representation Licorice 0.4 12.0 12.0 26 | mol selection {resname TRP and not hydrogen and chain A} 27 | mol color Type 28 | mol addrep top 29 | 30 | incr c 31 | 32 | } 33 | 34 | 35 | -------------------------------------------------------------------------------- /Analysis/job_reminder.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Job reminder script. 3 | # A simple script to help remind which jobs are running in which directories 4 | # by reading the input psf file from the configuration file, namd_equilibration_script.conf 5 | Red='\033[0;31m' # Red 6 | Lbl='\033[1;34m' # Light blue 7 | Yel='\033[0;33m' # Yellow 8 | Lgr='\033[0;37m' # Light gray 9 | NC='\033[0m' # No Color 10 | 11 | 12 | # Edit the list of job directories here: 13 | for job_dir in jobdir1 jobdir2 jobdir3 14 | 15 | do 16 | printf "\n${Yel} /$job_dir ${NC} Input files: \n" 17 | 18 | for d in ../$job_dir/*/ ; 19 | do 20 | (cd "$d" && printf " ${Lgr} $d: ${Lbl} " |tr -d "\n"; less namd_eq*| grep '.psf'| grep InputFiles | 21 | sed "s/structure //" | sed "s/ ..\/..\/InputFiles\///" ); 22 | done 23 | 24 | done 25 | printf "${NC}" 26 | -------------------------------------------------------------------------------- /Analysis/model_loader.vmd: -------------------------------------------------------------------------------- 1 | # Basic vmd model loader 2 | mol new /flush1/kui00b/MD_workflow_py/InputFiles/ChangeMe.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 3 | mol addfile /flush1/kui00b/MD_workflow_py/InputFiles/ChangeMe.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 4 | -------------------------------------------------------------------------------- /Analysis/sort.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Trajectory sorting template 3 | 4 | # Simple template for sorting output from main fileloader 5 | # Usually would first run 'gather' (./mdwf -g from top directory) 6 | # to generate dcd_trajectory_fileloader.vmd in /Analysis 7 | # then run ./sort.sh here. 8 | 9 | less dcd_trajectory_fileloader.vmd |grep SEL_001 > sel_001.vmd 10 | less dcd_trajectory_fileloader.vmd |grep SEL_002 > sel_002.vmd 11 | less dcd_trajectory_fileloader.vmd |grep SEL_003 > sel_003.vmd 12 | less dcd_trajectory_fileloader.vmd |grep SEL_004 > sel_004.vmd 13 | less dcd_trajectory_fileloader.vmd |grep SEL_005 > sel_005.vmd 14 | less dcd_trajectory_fileloader.vmd |grep SEL_006 > sel_006.vmd 15 | less dcd_trajectory_fileloader.vmd |grep SEL_007 > sel_007.vmd 16 | less dcd_trajectory_fileloader.vmd |grep SEL_008 > sel_008.vmd 17 | 18 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/ala.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N ALAXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C ALAXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O ALAXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA ALAXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB ALAXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | END 8 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/arg.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N ARGXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C ARGXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O ARGXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA ARGXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB ARGXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 CG ARGXA 1 -2.958 0.635 -1.914 0.80 0.00 A C 8 | ATOM 14 CD ARGXA 1 -3.871 1.173 -3.030 0.80 0.00 A C 9 | ATOM 17 NE ARGXA 1 -4.968 0.165 -3.227 0.80 0.00 A N 10 | ATOM 19 CZ ARGXA 1 -5.947 0.318 -4.129 0.80 0.00 A C 11 | ATOM 20 NH1 ARGXA 1 -6.870 -0.638 -4.220 0.80 0.00 A N 12 | ATOM 23 NH2 ARGXA 1 -6.033 1.394 -4.905 0.80 0.00 A N 13 | END 14 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/asn.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N ASNXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C ASNXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O ASNXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA ASNXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB ASNXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 CG ASNXA 1 -2.961 2.420 -1.261 0.80 0.00 A C 8 | ATOM 12 OD1 ASNXA 1 -3.423 2.465 -0.089 0.80 0.00 A O 9 | ATOM 13 ND2 ASNXA 1 -3.381 3.148 -2.300 0.80 0.00 A N 10 | END 11 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/asp.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N ASPXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C ASPXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O ASPXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA ASPXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB ASPXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 CG ASPXA 1 -2.839 2.638 -1.460 0.80 0.00 A C 8 | ATOM 12 OD1 ASPXA 1 -3.367 2.888 -0.311 0.80 0.00 A O 9 | ATOM 13 OD2 ASPXA 1 -3.200 3.309 -2.499 0.80 0.00 A O 10 | END 11 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/cys.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N CYSXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C CYSXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O CYSXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA CYSXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB CYSXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 SG CYSXA 1 -3.597 1.588 -1.473 0.80 0.00 A S 8 | END 9 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/gln.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N GLNXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C GLNXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O GLNXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA GLNXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB GLNXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 CG GLNXA 1 -2.629 0.524 -2.355 0.80 0.00 A C 8 | ATOM 14 CD GLNXA 1 -3.303 1.185 -3.569 0.80 0.00 A C 9 | ATOM 15 OE1 GLNXA 1 -2.992 2.299 -4.003 0.80 0.00 A O 10 | ATOM 16 NE2 GLNXA 1 -4.280 0.532 -4.139 0.80 0.00 A N 11 | END 12 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/glu.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N GLUXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C GLUXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O GLUXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA GLUXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB GLUXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 CG GLUXA 1 -1.624 1.461 -3.108 0.80 0.00 A C 8 | ATOM 14 CD GLUXA 1 -2.886 1.748 -3.863 0.80 0.00 A C 9 | ATOM 15 OE1 GLUXA 1 -3.892 1.033 -3.627 0.80 0.00 A O 10 | ATOM 16 OE2 GLUXA 1 -2.851 2.728 -4.655 0.80 0.00 A O 11 | END 12 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/gly.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N GLYXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C GLYXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O GLYXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA GLYXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | END 7 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/his.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N HISXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C HISXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O HISXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA HISXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB HISXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 ND1 HISXA 1 -2.933 0.927 -3.783 0.80 0.00 A N 8 | ATOM 12 CG HISXA 1 -2.497 0.555 -2.515 0.80 0.00 A C 9 | ATOM 13 CE1 HISXA 1 -3.510 -0.119 -4.348 0.80 0.00 A C 10 | ATOM 15 NE2 HISXA 1 -3.467 -1.130 -3.519 0.80 0.00 A N 11 | ATOM 17 CD2 HISXA 1 -2.846 -0.756 -2.368 0.80 0.00 A C 12 | END 13 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/ile.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N ILEXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C ILEXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O ILEXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA ILEXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB ILEXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 10 CG2 ILEXA 1 -1.809 3.010 -2.054 0.80 0.00 A C 8 | ATOM 14 CG1 ILEXA 1 -2.022 0.698 -2.821 0.80 0.00 A C 9 | ATOM 17 CD ILEXA 1 -1.001 0.954 -3.925 0.80 0.00 A C 10 | END 11 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/leu.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N LEUXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C LEUXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O LEUXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA LEUXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB LEUXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 CG LEUXA 1 -1.852 2.989 -2.108 0.80 0.00 A C 8 | ATOM 13 CD1 LEUXA 1 -3.165 3.288 -2.811 0.80 0.00 A C 9 | ATOM 17 CD2 LEUXA 1 -1.682 3.994 -0.974 0.80 0.00 A C 10 | END 11 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/lys.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N LYSXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C LYSXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O LYSXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA LYSXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB LYSXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 CG LYSXA 1 -1.540 1.988 -3.019 0.80 0.00 A C 8 | ATOM 14 CD LYSXA 1 -2.369 3.185 -3.437 0.80 0.00 A C 9 | ATOM 17 CE LYSXA 1 -2.173 3.566 -4.900 0.80 0.00 A C 10 | ATOM 20 NZ LYSXA 1 -2.691 2.568 -5.854 0.80 0.00 A N 11 | END 12 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/met.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N METXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C METXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O METXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA METXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB METXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 CG METXA 1 -3.266 1.647 -1.260 0.80 0.00 A C 8 | ATOM 14 SD METXA 1 -3.610 3.100 -0.236 0.80 0.00 A S 9 | ATOM 15 CE METXA 1 -5.382 3.346 -0.566 0.80 0.00 A C 10 | END 11 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/phe.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N PHEXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C PHEXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O PHEXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA PHEXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB PHEXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 CG PHEXA 1 -2.401 2.917 -1.833 0.80 0.00 A C 8 | ATOM 12 CD1 PHEXA 1 -2.088 4.000 -1.002 0.80 0.00 A C 9 | ATOM 14 CE1 PHEXA 1 -2.664 5.252 -1.245 0.80 0.00 A C 10 | ATOM 16 CZ PHEXA 1 -3.551 5.416 -2.317 0.80 0.00 A C 11 | ATOM 18 CD2 PHEXA 1 -3.286 3.078 -2.901 0.80 0.00 A C 12 | ATOM 20 CE2 PHEXA 1 -3.862 4.329 -3.144 0.80 0.00 A C 13 | END 14 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/pro.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N PROXA 1 1.300 0.000 0.000 0.80 0.00 A N 3 | ATOM 2 CD PROXA 1 2.140 0.790 0.924 0.80 0.00 A C 4 | ATOM 5 CA PROXA 1 2.126 -0.790 -0.924 0.80 0.00 A C 5 | ATOM 7 CB PROXA 1 3.515 -0.173 -0.747 0.80 0.00 A C 6 | ATOM 10 CG PROXA 1 3.525 0.216 0.701 0.80 0.00 A C 7 | ATOM 13 C PROXA 1 2.147 -2.305 -0.801 0.80 0.00 A C 8 | ATOM 14 O PROXA 1 2.921 -2.970 -1.488 0.80 0.00 A O 9 | END 10 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/ser.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N SERXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C SERXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O SERXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA SERXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB SERXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 OG SERXA 1 -3.069 1.943 -1.141 0.80 0.00 A O 8 | END 9 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/thr.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N THRXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C THRXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O THRXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA THRXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB THRXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 10 OG1 THRXA 1 -2.733 0.524 -1.832 0.80 0.00 A O 8 | ATOM 12 CG2 THRXA 1 -1.372 2.130 -2.940 0.80 0.00 A C 9 | END 10 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/trp.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N TRPXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C TRPXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O TRPXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA TRPXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB TRPXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 CG TRPXA 1 -2.058 2.937 -2.019 0.80 0.00 A C 8 | ATOM 12 CD1 TRPXA 1 -1.964 3.428 -3.293 0.80 0.00 A C 9 | ATOM 14 NE1 TRPXA 1 -2.260 4.759 -3.301 0.80 0.00 A N 10 | ATOM 16 CE2 TRPXA 1 -2.556 5.152 -2.003 0.80 0.00 A C 11 | ATOM 17 CD2 TRPXA 1 -2.426 4.014 -1.171 0.80 0.00 A C 12 | ATOM 18 CE3 TRPXA 1 -2.642 4.115 0.204 0.80 0.00 A C 13 | ATOM 20 CZ3 TRPXA 1 -3.005 5.334 0.717 0.80 0.00 A C 14 | ATOM 22 CZ2 TRPXA 1 -2.943 6.365 -1.474 0.80 0.00 A C 15 | ATOM 24 CH2 TRPXA 1 -3.153 6.459 -0.113 0.80 0.00 A C 16 | END 17 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/tyr.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N TYRXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C TYRXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O TYRXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA TYRXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB TYRXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 11 CG TYRXA 1 -2.611 2.797 -1.631 0.80 0.00 A C 8 | ATOM 12 CD1 TYRXA 1 -2.263 4.013 -1.027 0.80 0.00 A C 9 | ATOM 14 CE1 TYRXA 1 -3.078 5.143 -1.127 0.80 0.00 A C 10 | ATOM 16 CZ TYRXA 1 -4.246 5.023 -1.883 0.80 0.00 A C 11 | ATOM 17 OH TYRXA 1 -5.136 6.028 -2.029 0.80 0.00 A O 12 | ATOM 19 CD2 TYRXA 1 -3.782 2.719 -2.381 0.80 0.00 A C 13 | ATOM 21 CE2 TYRXA 1 -4.600 3.833 -2.521 0.80 0.00 A C 14 | END 15 | -------------------------------------------------------------------------------- /BUILD_DIR/AminoAcids/val.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N VALXA 1 -0.132 2.450 -0.112 0.80 0.00 A N 3 | ATOM 2 C VALXA 1 0.350 0.332 -1.257 0.80 0.00 A C 4 | ATOM 3 O VALXA 1 0.543 0.360 -2.471 0.80 0.00 A O 5 | ATOM 4 CA VALXA 1 -0.701 1.208 -0.598 0.80 0.00 A C 6 | ATOM 5 CB VALXA 1 -1.780 1.545 -1.584 0.80 0.00 A C 7 | ATOM 10 CG1 VALXA 1 -2.927 2.387 -1.014 0.80 0.00 A C 8 | ATOM 14 CG2 VALXA 1 -1.332 2.072 -2.941 0.80 0.00 A C 9 | END 10 | -------------------------------------------------------------------------------- /BUILD_DIR/ProcessScript_example.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Process Script Example Oct 2021 M kKuiper 3 | # A better way,.... 4 | 5 | # This process script is designed to automate the reliable replication of any 6 | # modelliing process, including mdel building and trajectory analysis. 7 | 8 | # Building models and performing analysis typically involve a series of complex operations 9 | # that may be hard to reproduce accurately without a script. 10 | 11 | # This process script is an example for running a sequential scripts to build 12 | # various models and prepare input for production runs. 13 | 14 | # Dependencies: bash, python3, VMD, NAMD 15 | 16 | run=01 # for different runs 17 | home=/scratch1/kui001/NewMouse_2021/ 18 | 19 | for i in model_01 model_02 model_03 20 | 21 | do 22 | 23 | # Build model with VMD (must have already prepared build_ scripts, ie) build_model_01, etc) 24 | echo " Building model:" 25 | vmd -dispdev text -e build_$i 26 | 27 | # Solvate model using hexagonal PBC with vmd script. 28 | echo "Solvating model:" 29 | vmd -dispdev text -e solvate_ionize_script.vmd 30 | 31 | # Optimize model (submits short NAMD job to queue and waits for completion) 32 | echo "Optimizing model:" 33 | sbatch --wait sbatch_optimization & 34 | wait 35 | echo "Done optimizing." 36 | 37 | # Process ionized dcd file -> Prepare production run 38 | echo "Preparing production input." 39 | vmd -dispdev text -e process_ionized_dcd.vmd 40 | cp ionized.psf $home/InputFiles/$i.psf 41 | cp ionized.pdb $home/InputFiles/$i.pdb 42 | 43 | 44 | 45 | 46 | 47 | ## Temmporary block: 48 | # Copy old input files back for new production: 49 | cp $home/InputFiles/$i.psf ionized.psf 50 | cp $home/InputFiles/$i.pdb ionized.pdb 51 | # Reporcess to set correct constraints: 52 | vmd -dispdev text -e $home/BUILD_DIR/process_ionized_dcd.vmd 53 | 54 | 55 | # Run production trajectory 56 | echo "Running production: $i " 57 | sbatch --wait $home/BUILD_DIR/sbatch_production & 58 | wait 59 | 60 | # Process production run to extract B and D chains 61 | rm evoef2_pdbfile.pdb # remove old data file 62 | vmd -dispdev text -e process_production_dcd.vmd 63 | cp evoef2_trajectory.pdb $home/BUILD_DIR/Output/Trajectory/$i.$run.pdb 64 | 65 | # Prepare Output data: 66 | echo "Run $run | `date`" >> $home/BUILD_DIR/Output/$i.txt 67 | 68 | # Process pdb trajectory with EvoEf2 script: 69 | echo "Procesing binding" 70 | python $home/BUILD_DIR/EvoEF2_processing_script_V1.py & 71 | wait 72 | 73 | cat temp_evoef2_data.txt >> $home/BUILD_DIR/Output/$i.txt 74 | 75 | done 76 | 77 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/2propanol.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 C2 PRO2A 1 2.426 0.656 0.167 1.00 0.00 A C 3 | ATOM 2 O2 PRO2A 1 3.564 0.049 0.599 1.00 0.00 A O 4 | ATOM 3 HO2 PRO2A 1 3.597 0.131 1.555 1.00 0.00 A H 5 | ATOM 4 H21 PRO2A 1 1.539 0.245 0.696 1.00 0.00 A H 6 | ATOM 5 C1 PRO2A 1 2.645 2.167 0.456 1.00 0.00 A C 7 | ATOM 6 H11 PRO2A 1 3.599 2.459 -0.034 1.00 0.00 A H 8 | ATOM 7 H12 PRO2A 1 1.860 2.806 -0.002 1.00 0.00 A H 9 | ATOM 8 H13 PRO2A 1 2.743 2.403 1.537 1.00 0.00 A H 10 | ATOM 9 C3 PRO2A 1 2.308 0.369 -1.361 1.00 0.00 A C 11 | ATOM 10 H31 PRO2A 1 2.665 -0.664 -1.559 1.00 0.00 A H 12 | ATOM 11 H32 PRO2A 1 1.257 0.541 -1.678 1.00 0.00 A H 13 | ATOM 12 H33 PRO2A 1 3.014 0.910 -2.027 1.00 0.00 A H 14 | END 15 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/3phosglycer.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 O1 3PG A 1 0.521 2.659 3.480 1.00 0.00 A O 3 | ATOM 2 C1 3PG A 1 -0.129 1.772 2.835 1.00 0.00 A C 4 | ATOM 3 O2 3PG A 1 -0.015 0.612 3.347 1.00 0.00 A O 5 | ATOM 4 C2 3PG A 1 -1.184 2.243 1.852 1.00 0.00 A C 6 | ATOM 5 O3 3PG A 1 -0.686 3.138 0.875 1.00 0.00 A O 7 | ATOM 6 C3 3PG A 1 -2.195 3.093 2.784 1.00 0.00 A C 8 | ATOM 7 H1 3PG A 1 -1.696 3.973 3.241 1.00 0.00 A H 9 | ATOM 8 H2 3PG A 1 -3.013 3.435 2.115 1.00 0.00 A H 10 | ATOM 9 O4 3PG A 1 -2.848 2.329 3.779 1.00 0.00 A O 11 | ATOM 10 P 3PG A 1 -2.420 2.226 5.336 1.00 0.00 A P 12 | ATOM 11 H3 3PG A 1 -0.565 3.956 1.363 1.00 0.00 A H 13 | ATOM 12 H4 3PG A 1 -1.702 1.391 1.363 1.00 0.00 A H 14 | ATOM 13 O5 3PG A 1 -1.178 3.010 5.486 1.00 0.00 A O 15 | ATOM 14 O6 3PG A 1 -1.671 0.931 5.460 1.00 0.00 A O 16 | ATOM 15 O7 3PG A 1 -3.528 2.360 6.307 1.00 0.00 A O 17 | ATOM 16 MG MG B 1 -0.185 1.655 4.878 1.00 0.00 B MG 18 | END 19 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/6phosgluc.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 C1 6PGLA 1 2.691 0.312 -0.295 1.00 0.00 A C 3 | ATOM 2 C2 6PGLA 1 2.664 1.803 0.205 1.00 0.00 A C 4 | ATOM 3 C3 6PGLA 1 1.581 2.688 -0.507 1.00 0.00 A C 5 | ATOM 4 C4 6PGLA 1 1.966 4.087 -0.992 1.00 0.00 A C 6 | ATOM 5 C5 6PGLA 1 2.698 4.210 -2.393 1.00 0.00 A C 7 | ATOM 6 C6 6PGLA 1 3.645 3.086 -2.679 1.00 0.00 A C 8 | ATOM 7 O1 6PGLA 1 3.853 -0.011 -1.016 1.00 0.00 A O 9 | ATOM 8 O2 6PGLA 1 3.999 2.351 0.183 1.00 0.00 A O 10 | ATOM 9 O3 6PGLA 1 0.457 2.698 0.369 1.00 0.00 A O 11 | ATOM 10 O4 6PGLA 1 3.322 5.503 -2.442 1.00 0.00 A O 12 | ATOM 11 O5 6PGLA 1 4.879 3.141 -2.307 1.00 0.00 A O 13 | ATOM 12 H1 6PGLA 1 1.748 0.087 -0.839 1.00 0.00 A H 14 | ATOM 13 H2 6PGLA 1 2.630 -0.238 0.668 1.00 0.00 A H 15 | ATOM 14 H3 6PGLA 1 2.279 1.743 1.245 1.00 0.00 A H 16 | ATOM 15 H4 6PGLA 1 1.222 2.102 -1.380 1.00 0.00 A H 17 | ATOM 16 O6 6PGLA 1 0.771 4.923 -1.119 1.00 0.00 A O 18 | ATOM 17 H5 6PGLA 1 1.937 4.143 -3.200 1.00 0.00 A H 19 | ATOM 18 O7 6PGLA 1 3.267 1.934 -2.823 1.00 0.00 A O 20 | ATOM 19 P 6PGLA 1 5.242 -0.712 -0.531 1.00 0.00 A P 21 | ATOM 20 H6 6PGLA 1 4.287 2.458 1.093 1.00 0.00 A H 22 | ATOM 21 H7 6PGLA 1 0.040 3.549 0.215 1.00 0.00 A H 23 | ATOM 22 H8 6PGLA 1 4.096 5.429 -3.004 1.00 0.00 A H 24 | ATOM 23 H9 6PGLA 1 2.625 4.587 -0.249 1.00 0.00 A H 25 | ATOM 24 H10 6PGLA 1 1.019 5.838 -1.270 1.00 0.00 A H 26 | ATOM 25 O8 6PGLA 1 5.309 -0.524 1.008 1.00 0.00 A O 27 | ATOM 26 O9 6PGLA 1 5.903 0.400 -1.262 1.00 0.00 A O 28 | ATOM 27 H11 6PGLA 1 5.204 -1.381 1.426 1.00 0.00 A H 29 | ATOM 28 O10 6PGLA 1 5.291 -2.141 -0.837 1.00 0.00 A O 30 | ATOM 29 MG MG B 1 4.606 1.520 -1.601 1.00 0.00 B MG 31 | END 32 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/GSH.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/BUILD_DIR/SmallMolecules/GSH.pdb -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/Mol2/3phosglycerate.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ***** 3 | 15 14 0 0 0 4 | SMALL 5 | GASTEIGER 6 | 7 | @ATOM 8 | 1 O 2.8353 0.2228 -0.5878 O.co2 1 UNL1 -0.2434 9 | 2 C 1.9680 1.0058 -0.0908 C.2 1 UNL1 0.3862 10 | 3 O 2.0144 2.2811 -0.0942 O.co2 1 UNL1 -0.2434 11 | 4 C 0.7867 0.3896 0.7260 C.3 1 UNL1 0.1797 12 | 5 O 0.9401 -1.0330 0.9886 O.3 1 UNL1 -0.3784 13 | 6 C -0.5870 0.6870 0.1018 C.3 1 UNL1 0.0967 14 | 7 H -1.2323 1.1234 0.8726 H 1 UNL1 0.0597 15 | 8 H -0.5231 1.4074 -0.7196 H 1 UNL1 0.0597 16 | 9 O -1.1824 -0.5189 -0.3850 O.3 1 UNL1 -0.2704 17 | 10 P -2.8242 -0.6012 -0.3493 P.3 1 UNL1 0.5949 18 | 11 H 0.2060 -1.4155 0.4527 H 1 UNL1 0.2106 19 | 12 H 0.8367 0.8804 1.7063 H 1 UNL1 0.0735 20 | 13 O -3.2928 0.6418 -1.0945 O.3 1 UNL1 -0.1035 21 | 14 O -3.1709 -0.6073 1.1344 O.2 1 UNL1 -0.2110 22 | 15 O -3.1384 -1.9121 -1.0601 O.2 1 UNL1 -0.2110 23 | @BOND 24 | 1 1 2 ar 25 | 2 2 3 ar 26 | 3 2 4 1 27 | 4 4 5 1 28 | 5 4 6 1 29 | 6 6 7 1 30 | 7 6 8 1 31 | 8 6 9 1 32 | 9 9 10 1 33 | 10 5 11 1 34 | 11 12 4 1 35 | 12 13 10 1 36 | 13 10 14 2 37 | 14 15 10 2 38 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/Mol2/alanine.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ***** 3 | 13 12 0 0 0 4 | SMALL 5 | GASTEIGER 6 | 7 | @ATOM 8 | 1 HA 0.4688 1.4335 -0.2740 H 1 ALA1 0.0195 9 | 2 CA 0.3269 0.3981 0.0489 C.3 1 ALA1 0.0176 10 | 3 N 1.7127 -0.2012 0.2114 N.4 1 ALA1 0.3869 11 | 4 H1 2.4013 0.2750 -0.3729 H 1 ALA1 -0.0889 12 | 5 H2 1.5670 -1.1281 -0.2683 H 1 ALA1 -0.0889 13 | 6 CB -0.3950 0.3129 1.3792 C.3 1 ALA1 -0.0683 14 | 7 HB1 -1.3911 0.7631 1.3113 H 1 ALA1 0.0219 15 | 8 HB2 0.1585 0.8423 2.1620 H 1 ALA1 0.0219 16 | 9 HB3 -0.5257 -0.7271 1.6994 H 1 ALA1 0.0219 17 | 10 C -0.4461 -0.4289 -1.0181 C.2 1 ALA1 0.3418 18 | 11 O 0.2477 -1.4526 -1.3351 O.co2 1 ALA1 -0.2483 19 | 12 OXT -1.5445 0.0133 -1.4119 O.co2 1 ALA1 -0.2483 20 | 13 H3 2.0219 -0.3673 1.1670 H 1 ALA1 -0.0889 21 | @BOND 22 | 1 1 2 1 23 | 2 2 3 1 24 | 3 2 6 1 25 | 4 2 10 1 26 | 5 3 4 1 27 | 6 3 5 1 28 | 7 6 7 1 29 | 8 6 8 1 30 | 9 6 9 1 31 | 10 10 11 ar 32 | 11 10 12 ar 33 | 12 13 3 1 34 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/Mol2/aspartate.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ***** 3 | 15 14 0 0 0 4 | SMALL 5 | GASTEIGER 6 | 7 | @ATOM 8 | 1 HA 0.2400 -1.4281 -0.1413 H 1 ASP1 0.0203 9 | 2 CA 0.3263 -0.3385 -0.2123 C.3 1 ASP1 0.0307 10 | 3 C 1.8060 0.1016 -0.0092 C.2 1 ASP1 0.3426 11 | 4 O 2.4498 -0.4540 0.9134 O.co2 1 ASP1 -0.2482 12 | 5 OXT 2.1802 0.9225 -0.9101 O.co2 1 ASP1 -0.2482 13 | 6 CB -0.5721 0.3570 0.8010 C.3 1 ASP1 0.0464 14 | 7 CG -2.0584 0.1563 0.5351 C.2 1 ASP1 0.3550 15 | 8 HB1 -0.3432 -0.0191 1.8061 H 1 ASP1 0.0368 16 | 9 N -0.1336 0.0153 -1.6114 N.4 1 ASP1 0.3874 17 | 10 H1 0.3334 -0.5679 -2.2985 H 1 ASP1 -0.0889 18 | 11 H2 0.1710 0.9849 -1.7571 H 1 ASP1 -0.0889 19 | 12 OD1 -2.3378 -0.2430 -0.6409 O.co2 1 ASP1 -0.2464 20 | 13 OD2 -2.8327 0.4733 1.4717 O.co2 1 ASP1 -0.2464 21 | 14 HB2 -0.3755 1.4365 0.8142 H 1 ASP1 0.0368 22 | 15 H3 -1.1759 -0.0839 -1.6270 H 1 ASP1 -0.0889 23 | @BOND 24 | 1 1 2 1 25 | 2 2 3 1 26 | 3 2 6 1 27 | 4 2 9 1 28 | 5 3 4 ar 29 | 6 3 5 ar 30 | 7 6 8 1 31 | 8 9 10 1 32 | 9 9 11 1 33 | 10 6 7 1 34 | 11 7 12 ar 35 | 12 7 13 ar 36 | 13 6 14 1 37 | 14 15 9 1 38 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/Mol2/citrate.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ***** 3 | 18 17 0 0 0 4 | SMALL 5 | GASTEIGER 6 | 7 | @ATOM 8 | 1 O 3.2311 0.2112 -0.5975 O.co2 1 UNL1 -0.2463 9 | 2 C 2.2811 0.4999 -1.3880 C.2 1 UNL1 0.3593 10 | 3 O 2.3912 1.0938 -2.5089 O.co2 1 UNL1 -0.2463 11 | 4 C 0.9120 -0.1475 -1.1076 C.3 1 UNL1 0.0890 12 | 5 H 0.3069 -0.0010 -2.0137 H 1 UNL1 0.0413 13 | 6 H 1.1288 -1.2254 -1.0671 H 1 UNL1 0.0413 14 | 7 C 0.0383 0.2070 0.1206 C.3 1 UNL1 0.1867 15 | 8 O 0.7588 -0.1963 1.3175 O.3 1 UNL1 -0.3764 16 | 9 C -0.2256 1.7652 0.1744 C.2 1 UNL1 0.3880 17 | 10 C -1.2683 -0.6159 0.0542 C.3 1 UNL1 0.0890 18 | 11 H -1.7842 -0.3817 -0.8877 H 1 UNL1 0.0413 19 | 12 H -0.9949 -1.6792 -0.0175 H 1 UNL1 0.0413 20 | 13 C -2.3370 -0.5553 1.1598 C.2 1 UNL1 0.3593 21 | 14 O -3.3527 0.1707 0.9287 O.co2 1 UNL1 -0.2463 22 | 15 O -2.2200 -1.4017 2.1033 O.co2 1 UNL1 -0.2463 23 | 16 O 0.2487 2.3274 1.2218 O.co2 1 UNL1 -0.2431 24 | 17 O -0.8367 2.3003 -0.7963 O.co2 1 UNL1 -0.2431 25 | 18 H 0.9336 0.6805 1.7343 H 1 UNL1 0.2109 26 | @BOND 27 | 1 1 2 ar 28 | 2 2 3 ar 29 | 3 2 4 1 30 | 4 4 5 1 31 | 5 4 6 1 32 | 6 4 7 1 33 | 7 7 8 1 34 | 8 7 9 1 35 | 9 7 10 1 36 | 10 10 11 1 37 | 11 10 12 1 38 | 12 10 13 1 39 | 13 13 14 ar 40 | 14 13 15 ar 41 | 15 9 16 ar 42 | 16 9 17 ar 43 | 17 8 18 1 44 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/Mol2/citrulline.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ***** 3 | 25 24 0 0 0 4 | SMALL 5 | GASTEIGER 6 | 7 | @ATOM 8 | 1 C 0.9954 -0.7350 -1.9742 C.2 1 UNL1 0.3420 9 | 2 CA 0.6083 -0.8058 -0.4655 C.3 1 UNL1 0.0206 10 | 3 C 0.4141 0.6008 0.0953 C.3 1 UNL1 -0.0546 11 | 4 H 1.3154 1.2024 -0.0781 H 1 UNL1 0.0255 12 | 5 H -0.3821 1.0999 -0.4695 H 1 UNL1 0.0255 13 | 6 C 0.1215 0.5982 1.6013 C.3 1 UNL1 -0.0383 14 | 7 H -0.3753 -0.3252 1.9161 H 1 UNL1 0.0280 15 | 8 H 1.0762 0.6045 2.1427 H 1 UNL1 0.0280 16 | 9 C -0.7116 1.7918 2.0664 C.3 1 UNL1 0.0130 17 | 10 N -1.9860 2.0059 1.3963 N.am 1 UNL1 -0.2996 18 | 11 C -2.8275 1.0306 0.9579 C.2 1 UNL1 0.2971 19 | 12 H -2.4481 2.8763 1.6212 H 1 UNL1 0.1502 20 | 13 N -0.6856 -1.5894 -0.3298 N.4 1 UNL1 0.3871 21 | 14 O 2.0531 -0.1421 -2.2756 O.co2 1 UNL1 -0.2483 22 | 15 OXT 0.1148 -1.3416 -2.6710 O.co2 1 UNL1 -0.2483 23 | 16 HA 1.3693 -1.3664 0.0870 H 1 UNL1 0.0198 24 | 17 H1 -0.9325 -1.7373 -1.3393 H 1 UNL1 -0.0889 25 | 18 H2 -1.4720 -1.0741 0.1037 H 1 UNL1 -0.0889 26 | 19 H3 -0.5641 -2.5137 0.0774 H 1 UNL1 -0.0889 27 | 20 H -0.1384 2.7169 1.9406 H 1 UNL1 0.0462 28 | 21 H -0.9310 1.6851 3.1346 H 1 UNL1 0.0462 29 | 22 N -4.0063 1.5338 0.5167 N.am 1 UNL1 -0.3134 30 | 23 H -4.6119 0.8566 0.0690 H 1 UNL1 0.1465 31 | 24 H -3.9844 2.4349 0.0591 H 1 UNL1 0.1465 32 | 25 O -2.5849 -0.1681 0.9015 O.2 1 UNL1 -0.2531 33 | @BOND 34 | 1 1 2 1 35 | 2 2 3 1 36 | 3 3 4 1 37 | 4 3 5 1 38 | 5 3 6 1 39 | 6 6 7 1 40 | 7 6 8 1 41 | 8 6 9 1 42 | 9 9 10 1 43 | 10 10 11 am 44 | 11 10 12 1 45 | 12 2 13 1 46 | 13 1 14 ar 47 | 14 1 15 ar 48 | 15 2 16 1 49 | 16 13 17 1 50 | 17 13 18 1 51 | 18 19 13 1 52 | 19 20 9 1 53 | 20 21 9 1 54 | 21 11 22 am 55 | 22 22 23 1 56 | 23 22 24 1 57 | 24 25 11 2 58 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/Mol2/glutamate.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ***** 3 | 18 17 0 0 0 4 | SMALL 5 | GASTEIGER 6 | 7 | @ATOM 8 | 1 C 2.1025 -0.6321 -1.2450 C.2 1 GLU1 0.3420 9 | 2 CA 0.7594 -0.7867 -0.4628 C.3 1 GLU1 0.0210 10 | 3 N -0.2919 -1.3117 -1.4359 N.4 1 GLU1 0.3871 11 | 4 CB 0.1885 0.4414 0.2288 C.3 1 GLU1 -0.0458 12 | 5 HB1 0.9403 0.8797 0.8961 H 1 GLU1 0.0259 13 | 6 HB2 -0.0352 1.2110 -0.5209 H 1 GLU1 0.0259 14 | 7 CG -1.0650 0.0962 1.0389 C.3 1 GLU1 0.0482 15 | 8 HG1 -1.7719 -0.4794 0.4296 H 1 GLU1 0.0378 16 | 9 HG2 -0.7809 -0.5405 1.8859 H 1 GLU1 0.0378 17 | 10 CD -1.8737 1.2763 1.5715 C.2 1 GLU1 0.3560 18 | 11 OE1 -1.5390 2.4134 1.1510 O.co2 1 GLU1 -0.2464 19 | 12 OE2 -2.8274 0.9342 2.3258 O.co2 1 GLU1 -0.2464 20 | 13 O 3.0686 -0.0767 -0.6796 O.co2 1 GLU1 -0.2483 21 | 14 OXT 1.9897 -1.1851 -2.3940 O.co2 1 GLU1 -0.2483 22 | 15 HA 0.9126 -1.6001 0.2567 H 1 GLU1 0.0198 23 | 16 H1 0.3136 -1.6941 -2.1987 H 1 GLU1 -0.0889 24 | 17 H2 -0.8062 -0.5311 -1.8502 H 1 GLU1 -0.0889 25 | 18 H3 -0.9016 -2.0197 -1.0347 H 1 GLU1 -0.0889 26 | @BOND 27 | 1 1 2 1 28 | 2 2 3 1 29 | 3 2 4 1 30 | 4 4 5 1 31 | 5 4 6 1 32 | 6 4 7 1 33 | 7 7 8 1 34 | 8 7 9 1 35 | 9 7 10 1 36 | 10 10 11 ar 37 | 11 10 12 ar 38 | 12 1 13 ar 39 | 13 1 14 ar 40 | 14 2 15 1 41 | 15 3 16 1 42 | 16 3 17 1 43 | 17 18 3 1 44 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/Mol2/glutamine.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ***** 3 | 20 19 0 0 0 4 | SMALL 5 | GASTEIGER 6 | 7 | @ATOM 8 | 1 C 1.4280 -0.4289 -1.9848 C.2 1 GLN1 0.3420 9 | 2 CA 0.9906 -0.7428 -0.5203 C.3 1 GLN1 0.0209 10 | 3 CB -0.0016 0.2779 0.0250 C.3 1 GLN1 -0.0477 11 | 4 HB1 0.4877 1.2600 0.0631 H 1 GLN1 0.0259 12 | 5 HB2 -0.8398 0.3863 -0.6758 H 1 GLN1 0.0259 13 | 6 CG -0.5376 -0.0724 1.4101 C.3 1 GLN1 0.0227 14 | 7 HG1 -1.2863 -0.8699 1.3457 H 1 GLN1 0.0358 15 | 8 HG2 0.2870 -0.4373 2.0349 H 1 GLN1 0.0358 16 | 9 CD -1.1645 1.0893 2.1523 C.2 1 GLN1 0.2104 17 | 10 OE1 -1.0645 1.2109 3.3687 O.2 1 GLN1 -0.2760 18 | 11 NE2 -1.9436 1.9396 1.4313 N.am 1 GLN1 -0.3293 19 | 12 HE21 -2.3098 2.7387 1.9363 H 1 GLN1 0.1449 20 | 13 HE22 -1.8680 2.0403 0.4281 H 1 GLN1 0.1449 21 | 14 N 0.3916 -2.1379 -0.5008 N.4 1 GLN1 0.3871 22 | 15 O 1.6079 0.7645 -2.2994 O.co2 1 GLN1 -0.2483 23 | 16 OXT 1.4531 -1.5190 -2.6483 O.co2 1 GLN1 -0.2483 24 | 17 HA 1.8913 -0.7989 0.1009 H 1 GLN1 0.0198 25 | 18 H1 0.8276 -2.5310 -1.3764 H 1 GLN1 -0.0889 26 | 19 H2 -0.6081 -2.1482 -0.7113 H 1 GLN1 -0.0889 27 | 20 H3 0.6607 -2.7222 0.2893 H 1 GLN1 -0.0889 28 | @BOND 29 | 1 1 2 1 30 | 2 2 3 1 31 | 3 3 4 1 32 | 4 3 5 1 33 | 5 3 6 1 34 | 6 6 7 1 35 | 7 6 8 1 36 | 8 6 9 1 37 | 9 9 10 2 38 | 10 9 11 am 39 | 11 11 12 1 40 | 12 11 13 1 41 | 13 2 14 1 42 | 14 1 15 ar 43 | 15 1 16 ar 44 | 16 2 17 1 45 | 17 14 18 1 46 | 18 14 19 1 47 | 19 20 14 1 48 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/Mol2/glycerate.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ***** 3 | 12 11 0 0 0 4 | SMALL 5 | GASTEIGER 6 | 7 | @ATOM 8 | 1 C 0.7176 0.7645 -0.3337 C.2 1 UNL1 0.3862 9 | 2 O 0.0136 1.7256 -0.7583 O.co2 1 UNL1 -0.2434 10 | 3 O 1.9076 0.7449 0.1079 O.co2 1 UNL1 -0.2434 11 | 4 C 0.0395 -0.6342 -0.3470 C.3 1 UNL1 0.1788 12 | 5 H 0.0211 -1.0011 -1.3785 H 1 UNL1 0.0735 13 | 6 O 0.8227 -1.5548 0.4500 O.3 1 UNL1 -0.3785 14 | 7 H 1.6580 -1.0410 0.5846 H 1 UNL1 0.2106 15 | 8 C -1.3624 -0.4864 0.2250 C.3 1 UNL1 0.0807 16 | 9 H -1.3641 0.1100 1.1449 H 1 UNL1 0.0588 17 | 10 H -1.7778 -1.4662 0.4822 H 1 UNL1 0.0588 18 | 11 O -2.2463 0.1359 -0.7113 O.3 1 UNL1 -0.3919 19 | 12 H -1.7658 0.9626 -0.9642 H 1 UNL1 0.2095 20 | @BOND 21 | 1 1 2 ar 22 | 2 1 3 ar 23 | 3 1 4 1 24 | 4 4 5 1 25 | 5 4 6 1 26 | 6 4 8 1 27 | 7 6 7 1 28 | 8 8 9 1 29 | 9 8 10 1 30 | 10 8 11 1 31 | 11 11 12 1 32 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/Mol2/malate.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ***** 3 | 13 12 0 0 0 4 | SMALL 5 | GASTEIGER 6 | 7 | @ATOM 8 | 1 O 2.9202 0.5373 0.2638 O.co2 1 UNL1 -0.2434 9 | 2 C 1.7889 0.7276 -0.3033 C.2 1 UNL1 0.3845 10 | 3 O 1.4706 1.6206 -1.1357 O.co2 1 UNL1 -0.2434 11 | 4 C 0.7059 -0.3256 0.1370 C.3 1 UNL1 0.1659 12 | 5 H 0.7651 -1.1328 -0.6003 H 1 UNL1 0.0717 13 | 6 O 1.1563 -0.8994 1.4066 O.3 1 UNL1 -0.3799 14 | 7 C -0.7163 0.1951 0.2960 C.3 1 UNL1 0.0857 15 | 8 H -0.8878 0.4806 1.3419 H 1 UNL1 0.0410 16 | 9 H -0.8556 1.0997 -0.3083 H 1 UNL1 0.0410 17 | 10 C -1.8662 -0.7310 -0.1111 C.2 1 UNL1 0.3590 18 | 11 O -1.5886 -1.8141 -0.6989 O.co2 1 UNL1 -0.2463 19 | 12 O -3.0231 -0.2866 0.1800 O.co2 1 UNL1 -0.2463 20 | 13 H 2.1074 -0.6346 1.4020 H 1 UNL1 0.2105 21 | @BOND 22 | 1 1 2 ar 23 | 2 2 3 ar 24 | 3 2 4 1 25 | 4 4 5 1 26 | 5 4 6 1 27 | 6 4 7 1 28 | 7 7 8 1 29 | 8 7 9 1 30 | 9 7 10 1 31 | 10 10 11 ar 32 | 11 10 12 ar 33 | 12 6 13 1 34 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/Mol2/valine.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ***** 3 | 19 18 0 0 0 4 | SMALL 5 | GASTEIGER 6 | 7 | @ATOM 8 | 1 HA 1.3980 0.0674 -0.8341 H 1 VAL1 0.0201 9 | 2 CA 0.4987 -0.4786 -0.5241 C.3 1 VAL1 0.0229 10 | 3 N 1.0291 -1.7236 0.1945 N.4 1 VAL1 0.3872 11 | 4 H1 0.3847 -2.0801 0.9013 H 1 VAL1 -0.0889 12 | 5 H2 0.9501 -2.4287 -0.5875 H 1 VAL1 -0.0889 13 | 6 CB -0.3293 0.3544 0.4701 C.3 1 VAL1 -0.0496 14 | 7 HB -1.2282 -0.2125 0.7459 H 1 VAL1 0.0285 15 | 8 CG1 -0.7919 1.6844 -0.1364 C.3 1 VAL1 -0.0637 16 | 9 HG11 0.0514 2.2467 -0.5512 H 1 VAL1 0.0232 17 | 10 HG12 -1.2755 2.3122 0.6204 H 1 VAL1 0.0232 18 | 11 HG13 -1.5286 1.5310 -0.9291 H 1 VAL1 0.0232 19 | 12 CG2 0.4526 0.6600 1.7567 C.3 1 VAL1 -0.0637 20 | 13 HG21 1.3869 1.1869 1.5343 H 1 VAL1 0.0232 21 | 14 HG22 0.6981 -0.2518 2.3096 H 1 VAL1 0.0232 22 | 15 HG23 -0.1378 1.2906 2.4307 H 1 VAL1 0.0232 23 | 16 C -0.2017 -0.9872 -1.8328 C.2 1 VAL1 0.3423 24 | 17 O -0.7913 -0.1632 -2.5570 O.co2 1 VAL1 -0.2482 25 | 18 OXT 0.0024 -2.2453 -1.9442 O.co2 1 VAL1 -0.2482 26 | 19 H3 2.0012 -1.6726 0.4911 H 1 VAL1 -0.0889 27 | @BOND 28 | 1 1 2 1 29 | 2 2 3 1 30 | 3 2 6 1 31 | 4 2 16 1 32 | 5 3 4 1 33 | 6 3 5 1 34 | 7 6 7 1 35 | 8 6 8 1 36 | 9 6 12 1 37 | 10 8 9 1 38 | 11 8 10 1 39 | 12 8 11 1 40 | 13 12 13 1 41 | 14 12 14 1 42 | 15 12 15 1 43 | 16 16 17 ar 44 | 17 16 18 ar 45 | 18 19 3 1 46 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/acetamide.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 CC ACEMA 1 -3.712 3.405 -4.184 1.00 0.00 A C 3 | ATOM 2 C ACEMA 1 -3.225 4.163 -5.383 1.00 0.00 A C 4 | ATOM 3 N ACEMA 1 -2.654 5.324 -5.139 1.00 0.00 A N 5 | ATOM 4 HC ACEMA 1 -2.899 5.824 -4.309 1.00 0.00 A H 6 | ATOM 5 HT ACEMA 1 -2.571 5.809 -6.009 1.00 0.00 A H 7 | ATOM 6 O ACEMA 1 -3.307 3.671 -6.479 1.00 0.00 A O 8 | ATOM 7 HC1 ACEMA 1 -4.504 2.710 -4.538 1.00 0.00 A H 9 | ATOM 8 HC2 ACEMA 1 -2.793 2.868 -3.866 1.00 0.00 A H 10 | ATOM 9 HC3 ACEMA 1 -4.036 4.123 -3.401 1.00 0.00 A H 11 | END 12 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/alanine.pdb: -------------------------------------------------------------------------------- 1 | COMPND UNNAMED 2 | AUTHOR GENERATED BY OPEN BABEL 2.3.90 3 | ATOM 1 HA ALAXA 1 0.469 1.433 -0.274 1.00 0.00 H 4 | ATOM 2 CA ALAXA 1 0.327 0.398 0.049 1.00 0.00 C 5 | ATOM 3 N ALAXA 1 1.713 -0.201 0.211 1.00 0.00 N 6 | ATOM 4 H1 ALAXA 1 2.401 0.275 -0.373 1.00 0.00 H 7 | ATOM 5 H2 ALAXA 1 1.567 -1.128 -0.268 1.00 0.00 H 8 | ATOM 6 CB ALAXA 1 -0.395 0.313 1.379 1.00 0.00 C 9 | ATOM 7 HB1 ALAXA 1 -1.391 0.763 1.311 1.00 0.00 H 10 | ATOM 8 HB2 ALAXA 1 0.158 0.842 2.162 1.00 0.00 H 11 | ATOM 9 HB3 ALAXA 1 -0.526 -0.727 1.699 1.00 0.00 H 12 | ATOM 10 C ALAXA 1 -0.446 -0.429 -1.018 1.00 0.00 C 13 | ATOM 11 O ALAXA 1 0.248 -1.453 -1.335 1.00 0.00 O 14 | ATOM 12 OXT ALAXA 1 -1.544 0.013 -1.412 1.00 0.00 O 15 | ATOM 13 H3 ALAXA 1 2.022 -0.367 1.167 1.00 0.00 H 16 | CONECT 1 2 17 | CONECT 2 1 3 6 10 18 | CONECT 3 2 4 5 13 19 | CONECT 4 3 20 | CONECT 5 3 21 | CONECT 6 2 7 8 9 22 | CONECT 7 6 23 | CONECT 8 6 24 | CONECT 9 6 25 | CONECT 10 2 11 12 26 | CONECT 11 10 27 | CONECT 12 10 28 | CONECT 13 3 29 | MASTER 0 0 0 0 0 0 0 0 13 0 13 0 30 | END 31 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/aspartate.pdb: -------------------------------------------------------------------------------- 1 | COMPND UNNAMED 2 | AUTHOR GENERATED BY OPEN BABEL 2.3.90 3 | ATOM 1 HA ASPXA 1 0.240 -1.428 -0.141 1.00 0.00 H 4 | ATOM 2 CA ASPXA 1 0.326 -0.338 -0.212 1.00 0.00 C 5 | ATOM 3 C ASPXA 1 1.806 0.102 -0.009 1.00 0.00 C 6 | ATOM 4 O ASPXA 1 2.450 -0.454 0.913 1.00 0.00 O 7 | ATOM 5 OXT ASPXA 1 2.180 0.923 -0.910 1.00 0.00 O 8 | ATOM 6 CB ASPXA 1 -0.572 0.357 0.801 1.00 0.00 C 9 | ATOM 7 CG ASPXA 1 -2.058 0.156 0.535 1.00 0.00 C 10 | ATOM 8 HB1 ASPXA 1 -0.343 -0.019 1.806 1.00 0.00 H 11 | ATOM 9 N ASPXA 1 -0.134 0.015 -1.611 1.00 0.00 N 12 | ATOM 10 H1 ASPXA 1 0.333 -0.568 -2.299 1.00 0.00 H 13 | ATOM 11 H2 ASPXA 1 0.171 0.985 -1.757 1.00 0.00 H 14 | ATOM 12 OD1 ASPXA 1 -2.338 -0.243 -0.641 1.00 0.00 O 15 | ATOM 13 OD2 ASPXA 1 -2.833 0.473 1.472 1.00 0.00 O 16 | ATOM 14 HB2 ASPXA 1 -0.375 1.436 0.814 1.00 0.00 H 17 | ATOM 15 H3 ASPXA 1 -1.176 -0.084 -1.627 1.00 0.00 H 18 | CONECT 1 2 19 | CONECT 2 1 3 6 9 20 | CONECT 3 2 4 5 21 | CONECT 4 3 22 | CONECT 5 3 23 | CONECT 6 2 8 7 14 24 | CONECT 7 6 12 13 25 | CONECT 8 6 26 | CONECT 9 2 10 11 15 27 | CONECT 10 9 28 | CONECT 11 9 29 | CONECT 12 7 30 | CONECT 13 7 31 | CONECT 14 6 32 | CONECT 15 9 33 | MASTER 0 0 0 0 0 0 0 0 15 0 15 0 34 | END 35 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/b_galactose.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 C1 BGALA 1 -7.885 -1.534 -3.308 1.00 0.00 A C 3 | ATOM 2 H1 BGALA 1 -7.985 -0.609 -3.915 1.00 0.00 A H 4 | ATOM 3 O1 BGALA 1 -8.270 -2.556 -4.171 1.00 0.00 A O 5 | ATOM 4 HO1 BGALA 1 -7.804 -3.343 -3.880 1.00 0.00 A H 6 | ATOM 5 C5 BGALA 1 -5.990 -1.059 -1.907 1.00 0.00 A C 7 | ATOM 6 H5 BGALA 1 -5.907 -0.039 -2.338 1.00 0.00 A H 8 | ATOM 7 O5 BGALA 1 -6.557 -1.885 -2.956 1.00 0.00 A O 9 | ATOM 8 C2 BGALA 1 -8.810 -1.476 -2.087 1.00 0.00 A C 10 | ATOM 9 H2 BGALA 1 -8.953 -2.429 -1.534 1.00 0.00 A H 11 | ATOM 10 O2 BGALA 1 -10.141 -1.076 -2.472 1.00 0.00 A O 12 | ATOM 11 HO2 BGALA 1 -10.425 -1.768 -3.073 1.00 0.00 A H 13 | ATOM 12 C3 BGALA 1 -8.276 -0.390 -1.198 1.00 0.00 A C 14 | ATOM 13 H3 BGALA 1 -8.190 0.570 -1.751 1.00 0.00 A H 15 | ATOM 14 O3 BGALA 1 -9.173 -0.172 -0.132 1.00 0.00 A O 16 | ATOM 15 HO3 BGALA 1 -10.018 -0.007 -0.556 1.00 0.00 A H 17 | ATOM 16 C4 BGALA 1 -6.821 -0.798 -0.699 1.00 0.00 A C 18 | ATOM 17 H4 BGALA 1 -6.349 0.056 -0.168 1.00 0.00 A H 19 | ATOM 18 O4 BGALA 1 -6.971 -1.847 0.235 1.00 0.00 A O 20 | ATOM 19 HO4 BGALA 1 -7.711 -1.547 0.769 1.00 0.00 A H 21 | ATOM 20 C6 BGALA 1 -4.560 -1.474 -1.577 1.00 0.00 A C 22 | ATOM 21 H61 BGALA 1 -4.004 -0.656 -1.072 1.00 0.00 A H 23 | ATOM 22 H62 BGALA 1 -3.966 -1.784 -2.464 1.00 0.00 A H 24 | ATOM 23 O6 BGALA 1 -4.497 -2.630 -0.681 1.00 0.00 A O 25 | ATOM 24 HO6 BGALA 1 -5.228 -2.649 -0.060 1.00 0.00 A H 26 | END 27 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/b_glucose.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 C1 BGLCA 1 -5.165 -0.630 -3.351 1.00 0.00 A C 3 | ATOM 2 H1 BGLCA 1 -4.687 0.267 -2.902 1.00 0.00 A H 4 | ATOM 3 O1 BGLCA 1 -5.993 -0.276 -4.418 1.00 0.00 A O 5 | ATOM 4 HO1 BGLCA 1 -6.316 -1.065 -4.860 1.00 0.00 A H 6 | ATOM 5 C5 BGLCA 1 -3.236 -1.744 -2.662 1.00 0.00 A C 7 | ATOM 6 H5 BGLCA 1 -2.880 -0.737 -2.357 1.00 0.00 A H 8 | ATOM 7 O5 BGLCA 1 -4.112 -1.485 -3.772 1.00 0.00 A O 9 | ATOM 8 C2 BGLCA 1 -5.919 -1.379 -2.235 1.00 0.00 A C 10 | ATOM 9 H2 BGLCA 1 -6.292 -2.314 -2.706 1.00 0.00 A H 11 | ATOM 10 O2 BGLCA 1 -7.072 -0.712 -1.745 1.00 0.00 A O 12 | ATOM 11 HO2 BGLCA 1 -7.784 -1.352 -1.681 1.00 0.00 A H 13 | ATOM 12 C3 BGLCA 1 -5.041 -1.831 -1.037 1.00 0.00 A C 14 | ATOM 13 H3 BGLCA 1 -4.716 -0.997 -0.379 1.00 0.00 A H 15 | ATOM 14 O3 BGLCA 1 -5.716 -2.736 -0.264 1.00 0.00 A O 16 | ATOM 15 HO3 BGLCA 1 -6.495 -2.419 0.198 1.00 0.00 A H 17 | ATOM 16 C4 BGLCA 1 -3.800 -2.574 -1.492 1.00 0.00 A C 18 | ATOM 17 H4 BGLCA 1 -4.034 -3.600 -1.846 1.00 0.00 A H 19 | ATOM 18 O4 BGLCA 1 -2.808 -2.734 -0.456 1.00 0.00 A O 20 | ATOM 19 HO4 BGLCA 1 -3.281 -3.222 0.222 1.00 0.00 A H 21 | ATOM 20 C6 BGLCA 1 -2.012 -2.398 -3.239 1.00 0.00 A C 22 | ATOM 21 H61 BGLCA 1 -1.328 -2.548 -2.376 1.00 0.00 A H 23 | ATOM 22 H62 BGLCA 1 -1.509 -1.621 -3.853 1.00 0.00 A H 24 | ATOM 23 O6 BGLCA 1 -2.218 -3.703 -3.806 1.00 0.00 A O 25 | ATOM 24 HO6 BGLCA 1 -2.806 -3.611 -4.559 1.00 0.00 A H 26 | END 27 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/benzene.pdb: -------------------------------------------------------------------------------- 1 | REMARK benzene 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | ATOM 1 CG BENZA 1 1.262 5.544 1.185 1.00 0.00 A C 4 | ATOM 2 HG BENZA 1 1.304 6.061 2.133 1.00 0.00 A H 5 | ATOM 3 CD1 BENZA 1 0.845 6.191 -0.018 1.00 0.00 A C 6 | ATOM 4 HD1 BENZA 1 0.545 7.226 0.062 1.00 0.00 A H 7 | ATOM 5 CD2 BENZA 1 1.665 4.156 1.046 1.00 0.00 A C 8 | ATOM 6 HD2 BENZA 1 1.872 3.601 1.950 1.00 0.00 A H 9 | ATOM 7 CE1 BENZA 1 0.830 5.461 -1.252 0.00 0.00 A C 10 | ATOM 8 HE1 BENZA 1 0.519 5.919 -2.179 0.00 0.00 A H 11 | ATOM 9 CE2 BENZA 1 1.792 3.514 -0.165 0.00 0.00 A C 12 | ATOM 10 HE2 BENZA 1 2.106 2.482 -0.113 0.00 0.00 A H 13 | ATOM 11 CZ BENZA 1 1.368 4.123 -1.367 1.00 0.00 A C 14 | ATOM 12 HZ BENZA 1 1.538 3.657 -2.326 1.00 0.00 A H 15 | END 16 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/benzoate.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 CZ 3CB A 1 2.753 -0.439 -0.636 1.00 0.00 A C 3 | ATOM 2 CE1 3CB A 1 2.014 0.599 0.039 1.00 0.00 A C 4 | ATOM 3 CD1 3CB A 1 1.820 1.848 -0.619 1.00 0.00 A C 5 | ATOM 4 CG 3CB A 1 2.426 2.040 -1.884 1.00 0.00 A C 6 | ATOM 5 CE2 3CB A 1 3.334 -0.185 -1.874 1.00 0.00 A C 7 | ATOM 6 CD2 3CB A 1 3.203 1.016 -2.475 1.00 0.00 A C 8 | ATOM 7 HE1 3CB A 1 1.445 0.340 0.920 1.00 0.00 A H 9 | ATOM 8 HG 3CB A 1 2.315 3.005 -2.356 1.00 0.00 A H 10 | ATOM 9 HD2 3CB A 1 3.717 1.267 -3.391 1.00 0.00 A H 11 | ATOM 10 HE2 3CB A 1 3.784 -1.021 -2.388 1.00 0.00 A H 12 | ATOM 11 HZ 3CB A 1 2.829 -1.409 -0.169 1.00 0.00 A H 13 | ATOM 12 CD3 3CB A 1 1.144 3.042 0.065 1.00 0.00 A C 14 | ATOM 13 O1 3CB A 1 1.035 4.090 -0.577 1.00 0.00 A O 15 | ATOM 14 O2 3CB A 1 0.748 2.828 1.275 1.00 0.00 A O 16 | END 17 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/butane.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 H11 BUTAA 1 -3.167 -1.351 2.636 1.00 0.00 A H 3 | ATOM 2 H12 BUTAA 1 -2.906 -0.816 0.875 1.00 0.00 A H 4 | ATOM 3 H13 BUTAA 1 -2.107 -2.290 1.566 1.00 0.00 A H 5 | ATOM 4 C1 BUTAA 1 -2.455 -1.259 1.788 1.00 0.00 A C 6 | ATOM 5 H21 BUTAA 1 -1.725 0.732 2.453 1.00 0.00 A H 7 | ATOM 6 H22 BUTAA 1 -0.797 -0.767 3.030 1.00 0.00 A H 8 | ATOM 7 C2 BUTAA 1 -1.360 -0.287 2.201 1.00 0.00 A C 9 | ATOM 8 H31 BUTAA 1 -0.723 0.548 0.172 1.00 0.00 A H 10 | ATOM 9 H32 BUTAA 1 -0.056 -1.060 0.574 1.00 0.00 A H 11 | ATOM 10 C3 BUTAA 1 -0.378 -0.092 1.012 1.00 0.00 A C 12 | ATOM 11 H41 BUTAA 1 0.636 1.610 1.734 1.00 0.00 A H 13 | ATOM 12 H42 BUTAA 1 1.807 0.474 0.823 1.00 0.00 A H 14 | ATOM 13 H43 BUTAA 1 1.302 0.041 2.382 1.00 0.00 A H 15 | ATOM 14 C4 BUTAA 1 0.916 0.565 1.481 1.00 0.00 A C 16 | END 17 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/citrate.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 O1 CIT A 1 -0.018 3.811 7.202 1.00 0.00 A O 3 | ATOM 2 C1 CIT A 1 1.271 3.783 7.175 1.00 0.00 A C 4 | ATOM 3 O2 CIT A 1 2.013 4.608 7.757 1.00 0.00 A O 5 | ATOM 4 C2 CIT A 1 1.838 2.650 6.351 1.00 0.00 A C 6 | ATOM 5 H1 CIT A 1 2.479 3.035 5.529 1.00 0.00 A H 7 | ATOM 6 H2 CIT A 1 2.479 2.112 7.082 1.00 0.00 A H 8 | ATOM 7 C3 CIT A 1 0.861 1.589 5.728 1.00 0.00 A C 9 | ATOM 8 O3 CIT A 1 0.194 1.092 6.860 1.00 0.00 A O 10 | ATOM 9 C4 CIT A 1 -0.152 2.133 4.649 1.00 0.00 A C 11 | ATOM 10 C5 CIT A 1 1.657 0.438 5.138 1.00 0.00 A C 12 | ATOM 11 H3 CIT A 1 2.183 0.599 4.172 1.00 0.00 A H 13 | ATOM 12 H4 CIT A 1 2.458 0.209 5.873 1.00 0.00 A H 14 | ATOM 13 C6 CIT A 1 0.906 -0.854 5.153 1.00 0.00 A C 15 | ATOM 14 O4 CIT A 1 0.774 -1.361 4.014 1.00 0.00 A O 16 | ATOM 15 O5 CIT A 1 0.414 -1.303 6.225 1.00 0.00 A O 17 | ATOM 16 O6 CIT A 1 -1.401 2.123 4.896 1.00 0.00 A O 18 | ATOM 17 O7 CIT A 1 0.337 2.765 3.672 1.00 0.00 A O 19 | ATOM 18 H5 CIT A 1 0.341 0.144 6.834 1.00 0.00 A H 20 | ATOM 19 MG MG B 1 -0.987 2.540 6.571 1.00 0.00 B MG 21 | END 22 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/citrulline.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 C1 CTU A 1 1.871 -1.168 1.111 1.00 0.00 A C 3 | ATOM 2 CA CTU A 1 1.110 -2.109 0.124 1.00 0.00 A C 4 | ATOM 3 C2 CTU A 1 -0.298 -2.422 0.852 1.00 0.00 A C 5 | ATOM 4 H4 CTU A 1 -0.998 -2.824 0.088 1.00 0.00 A H 6 | ATOM 5 H5 CTU A 1 -0.200 -3.133 1.699 1.00 0.00 A H 7 | ATOM 6 C3 CTU A 1 -0.955 -1.173 1.404 1.00 0.00 A C 8 | ATOM 7 H6 CTU A 1 -0.535 -0.295 0.869 1.00 0.00 A H 9 | ATOM 8 H7 CTU A 1 -2.045 -1.186 1.187 1.00 0.00 A H 10 | ATOM 9 C4 CTU A 1 -0.954 -0.927 2.925 1.00 0.00 A C 11 | ATOM 10 N1 CTU A 1 -0.998 0.463 3.270 1.00 0.00 A N 12 | ATOM 11 C5 CTU A 1 0.057 1.177 3.788 1.00 0.00 A C 13 | ATOM 12 H8 CTU A 1 -1.921 0.824 3.378 1.00 0.00 A H 14 | ATOM 13 N2 CTU A 1 0.897 -1.432 -1.190 1.00 0.00 A N 15 | ATOM 14 O1 CTU A 1 2.059 -1.471 2.310 1.00 0.00 A O 16 | ATOM 15 OXT CTU A 1 2.341 -0.033 0.831 1.00 0.00 A O 17 | ATOM 16 HA CTU A 1 1.722 -3.018 -0.062 1.00 0.00 A H 18 | ATOM 17 H1 CTU A 1 1.682 -0.871 -1.577 1.00 0.00 A H 19 | ATOM 18 H2 CTU A 1 0.052 -0.826 -1.227 1.00 0.00 A H 20 | ATOM 19 H3 CTU A 1 0.691 -2.194 -1.868 1.00 0.00 A H 21 | ATOM 20 H9 CTU A 1 -0.086 -1.467 3.359 1.00 0.00 A H 22 | ATOM 21 H10 CTU A 1 -1.828 -1.367 3.450 1.00 0.00 A H 23 | ATOM 22 N3 CTU A 1 -0.199 2.399 4.157 1.00 0.00 A N 24 | ATOM 23 H11 CTU A 1 0.340 2.785 4.906 1.00 0.00 A H 25 | ATOM 24 H12 CTU A 1 -1.089 2.833 4.020 1.00 0.00 A H 26 | ATOM 25 O2 CTU A 1 1.214 0.792 3.797 1.00 0.00 A O 27 | ATOM 26 MG MG B 1 2.459 0.232 2.634 1.00 0.00 B MG 28 | END 29 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/coumarin.pdb: -------------------------------------------------------------------------------- 1 | REMARK coumarin 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | ATOM 1 C7 RIN A 1 -5.090 -1.114 -4.008 1.00 0.00 A C 4 | ATOM 2 C6 RIN A 1 -5.676 0.036 -4.508 1.00 0.00 A C 5 | ATOM 3 C5 RIN A 1 -5.176 1.266 -4.081 1.00 0.00 A C 6 | ATOM 4 C10 RIN A 1 -4.175 1.270 -3.201 1.00 0.00 A C 7 | ATOM 5 C9 RIN A 1 -3.589 0.098 -2.611 1.00 0.00 A C 8 | ATOM 6 C8 RIN A 1 -4.138 -1.105 -3.018 1.00 0.00 A C 9 | ATOM 7 H4 RIN A 1 -6.384 2.138 -5.460 1.00 0.00 A H 10 | ATOM 8 H7 RIN A 1 -5.574 -2.013 -4.360 1.00 0.00 A H 11 | ATOM 9 H6 RIN A 1 -6.419 -0.083 -5.282 1.00 0.00 A H 12 | ATOM 10 C4 RIN A 1 -5.637 2.389 -4.708 1.00 0.00 A C 13 | ATOM 11 H9 RIN A 1 -2.752 0.292 -1.957 1.00 0.00 A H 14 | ATOM 12 H8 RIN A 1 -3.845 -2.027 -2.538 1.00 0.00 A H 15 | ATOM 13 C3 RIN A 1 -5.127 3.664 -4.460 1.00 0.00 A C 16 | ATOM 14 H3 RIN A 1 -5.390 4.591 -4.970 1.00 0.00 A H 17 | ATOM 15 O1 RIN A 1 -3.549 2.523 -3.016 1.00 0.00 A O 18 | ATOM 16 C2 RIN A 1 -4.059 3.722 -3.532 1.00 0.00 A C 19 | ATOM 17 O2 RIN A 1 -3.413 4.725 -3.254 1.00 0.00 A O 20 | END 21 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/ethanol.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 C1 ETOHA 1 1.934 0.900 -0.404 1.00 0.00 A C 3 | ATOM 2 O1 ETOHA 1 1.702 2.295 -0.434 1.00 0.00 A O 4 | ATOM 3 HO1 ETOHA 1 2.528 2.712 -0.689 1.00 0.00 A H 5 | ATOM 4 H11 ETOHA 1 2.627 0.778 0.456 1.00 0.00 A H 6 | ATOM 5 H12 ETOHA 1 2.446 0.566 -1.332 1.00 0.00 A H 7 | ATOM 6 C2 ETOHA 1 0.553 0.269 -0.426 1.00 0.00 A C 8 | ATOM 7 H21 ETOHA 1 0.075 0.306 -1.428 1.00 0.00 A H 9 | ATOM 8 H22 ETOHA 1 0.530 -0.805 -0.143 1.00 0.00 A H 10 | ATOM 9 H23 ETOHA 1 -0.130 0.660 0.359 1.00 0.00 A H 11 | END 12 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/fruct16biphos.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 H1 FBP A 1 -1.405 3.386 7.108 1.00 0.00 A H 3 | ATOM 2 C1 FBP A 1 -0.531 2.772 6.842 1.00 0.00 A C 4 | ATOM 3 O1 FBP A 1 0.620 3.559 6.916 1.00 0.00 A O 5 | ATOM 4 C2 FBP A 1 -0.537 1.461 7.689 1.00 0.00 A C 6 | ATOM 5 O2 FBP A 1 0.736 0.782 7.679 1.00 0.00 A O 7 | ATOM 6 C3 FBP A 1 -0.885 1.634 9.198 1.00 0.00 A C 8 | ATOM 7 O3 FBP A 1 -1.505 0.566 7.100 1.00 0.00 A O 9 | ATOM 8 C4 FBP A 1 -1.658 0.883 5.675 1.00 0.00 A C 10 | ATOM 9 C5 FBP A 1 -1.322 -0.380 4.902 1.00 0.00 A C 11 | ATOM 10 H2 FBP A 1 -2.717 1.166 5.596 1.00 0.00 A H 12 | ATOM 11 C6 FBP A 1 -0.730 2.112 5.482 1.00 0.00 A C 13 | ATOM 12 H3 FBP A 1 0.310 1.802 5.298 1.00 0.00 A H 14 | ATOM 13 O4 FBP A 1 -1.096 3.080 4.404 1.00 0.00 A O 15 | ATOM 14 H4 FBP A 1 0.461 0.027 7.154 1.00 0.00 A H 16 | ATOM 15 H5 FBP A 1 0.850 3.771 7.824 1.00 0.00 A H 17 | ATOM 16 H6 FBP A 1 -1.289 3.864 4.924 1.00 0.00 A H 18 | ATOM 17 H7 FBP A 1 -2.022 -0.688 4.097 1.00 0.00 A H 19 | ATOM 18 H8 FBP A 1 -1.326 -1.250 5.593 1.00 0.00 A H 20 | ATOM 19 O5 FBP A 1 -0.011 -0.325 4.316 1.00 0.00 A O 21 | ATOM 20 H9 FBP A 1 -0.728 0.668 9.724 1.00 0.00 A H 22 | ATOM 21 H10 FBP A 1 -1.970 1.819 9.347 1.00 0.00 A H 23 | ATOM 22 O6 FBP A 1 -0.248 2.697 9.973 1.00 0.00 A O 24 | ATOM 23 P1 FBP A 1 1.352 2.701 10.405 1.00 0.00 A P 25 | ATOM 24 P2 FBP A 1 0.381 0.235 2.888 1.00 0.00 A P 26 | ATOM 25 O7 FBP A 1 1.205 1.517 3.120 1.00 0.00 A O 27 | ATOM 26 O8 FBP A 1 -0.833 1.014 2.411 1.00 0.00 A O 28 | ATOM 27 O9 FBP A 1 1.813 1.247 10.404 1.00 0.00 A O 29 | ATOM 28 O10 FBP A 1 1.771 3.646 11.484 1.00 0.00 A O 30 | ATOM 29 O11 FBP A 1 2.063 2.913 9.098 1.00 0.00 A O 31 | ATOM 30 O12 FBP A 1 0.872 -0.668 1.860 1.00 0.00 A O 32 | ATOM 31 MG MG B 1 -0.149 2.490 2.810 -1.00 0.00 B MG 33 | ATOM 32 MG MG B 1 2.316 1.194 8.800 1.00 0.00 B MG 34 | END 35 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/fructose_1_6_biphosphate.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 H1 FBP A 1 -1.262 0.705 2.085 1.00 0.00 A H 3 | ATOM 2 C1 FBP A 1 -0.945 0.285 1.120 1.00 0.00 A C 4 | ATOM 3 O1 FBP A 1 -1.898 0.701 0.089 1.00 0.00 A O 5 | ATOM 4 C2 FBP A 1 0.623 0.706 0.897 1.00 0.00 A C 6 | ATOM 5 O2 FBP A 1 0.827 0.872 -0.469 1.00 0.00 A O 7 | ATOM 6 C3 FBP A 1 0.904 2.003 1.610 1.00 0.00 A C 8 | ATOM 7 O3 FBP A 1 1.360 -0.344 1.527 1.00 0.00 A O 9 | ATOM 8 C4 FBP A 1 0.494 -1.452 1.886 1.00 0.00 A C 10 | ATOM 9 C5 FBP A 1 1.212 -2.777 1.596 1.00 0.00 A C 11 | ATOM 10 H2 FBP A 1 0.375 -1.466 2.980 1.00 0.00 A H 12 | ATOM 11 C6 FBP A 1 -0.943 -1.273 1.245 1.00 0.00 A C 13 | ATOM 12 H3 FBP A 1 -0.873 -1.775 0.268 1.00 0.00 A H 14 | ATOM 13 O4 FBP A 1 -1.985 -1.834 2.062 1.00 0.00 A O 15 | ATOM 14 H4 FBP A 1 0.714 1.789 -0.729 1.00 0.00 A H 16 | ATOM 15 H5 FBP A 1 -1.580 1.508 -0.321 1.00 0.00 A H 17 | ATOM 16 H6 FBP A 1 -1.689 -2.671 2.427 1.00 0.00 A H 18 | ATOM 17 H7 FBP A 1 2.006 -3.033 2.330 1.00 0.00 A H 19 | ATOM 18 H8 FBP A 1 1.738 -2.803 0.618 1.00 0.00 A H 20 | ATOM 19 O5 FBP A 1 0.356 -3.920 1.517 1.00 0.00 A O 21 | ATOM 20 H9 FBP A 1 1.951 2.357 1.494 1.00 0.00 A H 22 | ATOM 21 H10 FBP A 1 0.738 1.867 2.700 1.00 0.00 A H 23 | ATOM 22 O6 FBP A 1 0.089 3.147 1.260 1.00 0.00 A O 24 | ATOM 23 P1 FBP A 1 0.270 4.200 0.043 1.00 0.00 A P 25 | ATOM 24 P2 FBP A 1 -0.066 -4.856 2.905 1.00 0.00 A P 26 | ATOM 25 O7 FBP A 1 -0.381 -6.214 2.341 1.00 0.00 A O 27 | ATOM 26 O8 FBP A 1 -1.225 -4.084 3.523 1.00 0.00 A O 28 | ATOM 27 O9 FBP A 1 -0.142 3.409 -1.211 1.00 0.00 A O 29 | ATOM 28 O10 FBP A 1 1.762 4.627 0.030 1.00 0.00 A O 30 | ATOM 29 O11 FBP A 1 -0.826 5.287 0.322 1.00 0.00 A O 31 | ATOM 30 O12 FBP A 1 1.255 -4.828 3.717 1.00 0.00 A O 32 | END 33 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/glycerate.pdb: -------------------------------------------------------------------------------- 1 | COMPND UNNAMED 2 | AUTHOR GENERATED BY OPEN BABEL 2.3.90 3 | HETATM 1 C1 GLA 1 0.718 0.765 -0.334 1.00 0.00 C 4 | HETATM 2 O1 GLA 1 0.014 1.726 -0.758 1.00 0.00 O 5 | HETATM 3 O2 GLA 1 1.908 0.745 0.108 1.00 0.00 O 6 | HETATM 4 C2 GLA 1 0.039 -0.634 -0.347 1.00 0.00 C 7 | HETATM 5 H1 GLA 1 0.021 -1.001 -1.378 1.00 0.00 H 8 | HETATM 6 O3 GLA 1 0.823 -1.555 0.450 1.00 0.00 O 9 | HETATM 7 H2 GLA 1 1.658 -1.041 0.585 1.00 0.00 H 10 | HETATM 8 C3 GLA 1 -1.362 -0.486 0.225 1.00 0.00 C 11 | HETATM 9 H3 GLA 1 -1.364 0.110 1.145 1.00 0.00 H 12 | HETATM 10 H4 GLA 1 -1.778 -1.466 0.482 1.00 0.00 H 13 | HETATM 11 O4 GLA 1 -2.246 0.136 -0.711 1.00 0.00 O 14 | HETATM 12 H5 GLA 1 -1.766 0.963 -0.964 1.00 0.00 H 15 | CONECT 1 2 3 4 16 | CONECT 2 1 17 | CONECT 3 1 18 | CONECT 4 1 5 6 8 19 | CONECT 5 4 20 | CONECT 6 4 7 21 | CONECT 7 6 22 | CONECT 8 4 9 10 11 23 | CONECT 9 8 24 | CONECT 10 8 25 | CONECT 11 8 12 26 | CONECT 12 11 27 | MASTER 0 0 0 0 0 0 0 0 12 0 12 0 28 | END 29 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/hexoseP.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 C1 HEXPA 1 0.319 2.601 -1.833 1.00 0.00 A C 3 | ATOM 2 O1 HEXPA 1 -0.475 2.912 -0.739 1.00 0.00 A O 4 | ATOM 3 C2 HEXPA 1 -0.475 1.887 0.235 1.00 0.00 A C 5 | ATOM 4 C3 HEXPA 1 0.903 1.938 0.883 1.00 0.00 A C 6 | ATOM 5 O2 HEXPA 1 1.151 0.858 1.853 1.00 0.00 A O 7 | ATOM 6 C4 HEXPA 1 1.973 1.710 -0.231 1.00 0.00 A C 8 | ATOM 7 C5 HEXPA 1 1.743 2.715 -1.430 1.00 0.00 A C 9 | ATOM 8 O3 HEXPA 1 2.495 2.304 -2.523 1.00 0.00 A O 10 | ATOM 9 O4 HEXPA 1 3.272 1.702 0.314 1.00 0.00 A O 11 | ATOM 10 C6 HEXPA 1 -1.584 2.118 1.179 1.00 0.00 A C 12 | ATOM 11 O5 HEXPA 1 -2.810 1.996 0.489 1.00 0.00 A O 13 | ATOM 12 O6 HEXPA 1 -0.209 3.743 -2.568 1.00 0.00 A O 14 | ATOM 13 H1 HEXPA 1 -0.556 0.940 -0.340 1.00 0.00 A H 15 | ATOM 14 H2 HEXPA 1 1.016 2.904 1.419 1.00 0.00 A H 16 | ATOM 15 H3 HEXPA 1 1.790 0.671 -0.578 1.00 0.00 A H 17 | ATOM 16 H4 HEXPA 1 2.005 3.759 -1.155 1.00 0.00 A H 18 | ATOM 17 H5 HEXPA 1 -0.018 1.660 -2.319 1.00 0.00 A H 19 | ATOM 18 H6 HEXPA 1 0.314 3.662 -3.369 1.00 0.00 A H 20 | ATOM 19 H7 HEXPA 1 3.443 2.392 -2.393 1.00 0.00 A H 21 | ATOM 20 H8 HEXPA 1 3.227 1.036 1.004 1.00 0.00 A H 22 | ATOM 21 H9 HEXPA 1 -1.431 3.104 1.668 1.00 0.00 A H 23 | ATOM 22 H10 HEXPA 1 -1.629 1.344 1.975 1.00 0.00 A H 24 | ATOM 23 P HEXPA 1 -3.580 3.046 -0.370 1.00 0.00 A P 25 | ATOM 24 O7 HEXPA 1 -5.002 3.025 -0.096 1.00 0.00 A O 26 | ATOM 25 O8 HEXPA 1 -3.152 2.878 -1.764 1.00 0.00 A O 27 | ATOM 26 O9 HEXPA 1 -2.773 4.313 -0.162 1.00 0.00 A O 28 | ATOM 27 H11 HEXPA 1 0.528 0.847 2.584 1.00 0.00 A H 29 | ATOM 28 MG MG B 1 -1.862 4.033 -1.565 1.00 0.00 B MG 30 | END 31 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/imidazole.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 CG IMIAA 1 -0.507 -2.024 0.190 1.00 0.00 A C 3 | ATOM 2 HG IMIAA 1 -1.389 -2.002 0.818 1.00 0.00 A H 4 | ATOM 3 CD2 IMIAA 1 0.759 -2.378 0.514 1.00 0.00 A C 5 | ATOM 4 HD2 IMIAA 1 1.103 -2.755 1.470 1.00 0.00 A H 6 | ATOM 5 ND1 IMIAA 1 -0.393 -1.440 -1.055 1.00 0.00 A N 7 | ATOM 6 HD1 IMIAA 1 -1.163 -1.140 -1.635 1.00 0.00 A H 8 | ATOM 7 CE1 IMIAA 1 0.852 -1.666 -1.484 1.00 0.00 A C 9 | ATOM 8 HE1 IMIAA 1 1.248 -1.207 -2.390 1.00 0.00 A H 10 | ATOM 9 NE2 IMIAA 1 1.583 -2.227 -0.551 1.00 0.00 A N 11 | END 12 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/malate.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 O1 MAL A 1 -4.973 2.127 1.180 1.00 0.00 A O 3 | ATOM 2 C1 MAL A 1 -4.929 0.879 1.502 1.00 0.00 A C 4 | ATOM 3 O2 MAL A 1 -4.974 0.144 0.441 1.00 0.00 A O 5 | ATOM 4 C2 MAL A 1 -5.653 0.402 2.760 1.00 0.00 A C 6 | ATOM 5 H1 MAL A 1 -5.632 -0.705 2.669 1.00 0.00 A H 7 | ATOM 6 O3 MAL A 1 -5.024 0.879 3.970 1.00 0.00 A O 8 | ATOM 7 C3 MAL A 1 -7.252 0.823 2.791 1.00 0.00 A C 9 | ATOM 8 H2 MAL A 1 -7.938 0.061 3.220 1.00 0.00 A H 10 | ATOM 9 H3 MAL A 1 -7.320 1.714 3.453 1.00 0.00 A H 11 | ATOM 10 C4 MAL A 1 -7.741 1.166 1.450 1.00 0.00 A C 12 | ATOM 11 O4 MAL A 1 -7.634 0.304 0.568 1.00 0.00 A O 13 | ATOM 12 O5 MAL A 1 -7.628 2.344 0.956 1.00 0.00 A O 14 | ATOM 13 H4 MAL A 1 -5.295 1.800 3.963 1.00 0.00 A H 15 | ATOM 14 MG MG B 1 -6.247 1.461 -0.056 1.00 0.00 B MG 16 | END 17 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/methanol.pdb: -------------------------------------------------------------------------------- 1 | COMPND Methanol 2 | AUTHOR GENERATED BY OPEN BABEL 2.3.90 3 | HETATM 1 CB MEOH 1 -0.106 1.131 1.584 1.00 0.00 C 4 | HETATM 2 HG1 MEOH 1 0.986 1.118 1.569 1.00 0.00 H 5 | HETATM 3 OG MEOH 1 -0.562 2.471 1.624 1.00 0.00 O 6 | HETATM 4 HB1 MEOH 1 -0.476 0.593 2.460 1.00 0.00 H 7 | HETATM 5 HB2 MEOH 1 -0.487 0.653 0.678 1.00 0.00 H 8 | HETATM 6 HB3 MEOH 1 -0.209 2.869 2.437 1.00 0.00 H 9 | END 10 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/mg_ion.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 MG MG 1 5.000 5.000 5.000 1.00 0.00 A MG 3 | END 4 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/mol.pdb.bup: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N GLUXA 1 -0.399 -0.294 1.158 1.00 0.00 A N 3 | ATOM 2 HT1 GLUXA 1 -0.304 0.624 0.680 1.00 0.00 A H 4 | ATOM 3 HT2 GLUXA 1 -0.576 -1.152 0.598 1.00 0.00 A H 5 | ATOM 4 HT3 GLUXA 1 -1.122 -0.085 1.875 0.00 0.00 A 6 | ATOM 5 CA GLUXA 1 0.731 -0.572 2.198 1.00 0.00 A C 7 | ATOM 6 HA GLUXA 1 1.693 -0.181 1.900 1.00 0.00 A H 8 | ATOM 7 CB GLUXA 1 0.322 0.045 3.534 1.00 0.00 A C 9 | ATOM 8 HB1 GLUXA 1 -0.627 -0.375 3.931 1.00 0.00 A H 10 | ATOM 9 HB2 GLUXA 1 1.145 -0.088 4.269 1.00 0.00 A H 11 | ATOM 10 CG GLUXA 1 0.110 1.587 3.522 1.00 0.00 A C 12 | ATOM 11 HG1 GLUXA 1 -0.233 1.874 4.539 1.00 0.00 A H 13 | ATOM 12 HG2 GLUXA 1 1.011 2.202 3.314 1.00 0.00 A H 14 | ATOM 13 CD GLUXA 1 -1.003 1.903 2.545 1.00 0.00 A C 15 | ATOM 14 OE1 GLUXA 1 -0.766 2.760 1.668 1.00 0.00 A O 16 | ATOM 15 OE2 GLUXA 1 -1.994 1.123 2.505 1.00 0.00 A O 17 | ATOM 16 C GLUXA 1 1.050 -2.100 2.197 1.00 0.00 A C 18 | ATOM 17 OT1 GLUXA 1 0.410 -2.873 1.474 0.00 0.00 A 19 | ATOM 18 OT2 GLUXA 1 2.016 -2.493 2.895 0.00 0.00 A 20 | END 21 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/n_ben_acet.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 C1 NZADA 1 -6.981 8.938 0.373 1.00 0.00 A C 3 | ATOM 2 C2 NZADA 1 -6.621 8.185 -0.756 1.00 0.00 A C 4 | ATOM 3 C3 NZADA 1 -5.475 8.576 -1.518 1.00 0.00 A C 5 | ATOM 4 C4 NZADA 1 -4.891 9.802 -1.350 1.00 0.00 A C 6 | ATOM 5 C5 NZADA 1 -5.185 10.514 -0.157 1.00 0.00 A C 7 | ATOM 6 C6 NZADA 1 -6.147 10.013 0.724 1.00 0.00 A C 8 | ATOM 7 H2 NZADA 1 -7.050 7.252 -1.090 1.00 0.00 A H 9 | ATOM 8 H3 NZADA 1 -5.156 7.920 -2.315 1.00 0.00 A H 10 | ATOM 9 H4 NZADA 1 -4.122 10.176 -2.010 1.00 0.00 A H 11 | ATOM 10 H5 NZADA 1 -4.597 11.322 0.252 1.00 0.00 A H 12 | ATOM 11 H6 NZADA 1 -6.339 10.420 1.706 1.00 0.00 A H 13 | ATOM 12 C7 NZADA 1 -8.034 8.561 1.361 1.00 0.00 A C 14 | ATOM 13 H71 NZADA 1 -8.926 8.161 0.834 1.00 0.00 A H 15 | ATOM 14 H72 NZADA 1 -8.421 9.441 1.917 1.00 0.00 A H 16 | ATOM 15 N8 NZADA 1 -7.534 7.601 2.287 1.00 0.00 A N 17 | ATOM 16 H8 NZADA 1 -6.825 7.052 1.851 1.00 0.00 A H 18 | ATOM 17 C9 NZADA 1 -7.389 7.834 3.608 1.00 0.00 A C 19 | ATOM 18 O9 NZADA 1 -7.809 8.797 4.247 1.00 0.00 A O 20 | ATOM 19 C10 NZADA 1 -6.798 6.680 4.365 1.00 0.00 A C 21 | ATOM 20 H101 NZADA 1 -6.883 6.926 5.445 0.00 0.00 A H 22 | ATOM 21 H102 NZADA 1 -5.723 6.689 4.083 0.00 0.00 A H 23 | ATOM 22 H103 NZADA 1 -7.123 5.631 4.193 0.00 0.00 A H 24 | END 25 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/n_benzylacetamide.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 C1 NZADA 1 -6.981 8.938 0.373 1.00 0.00 A C 3 | ATOM 2 C2 NZADA 1 -6.621 8.185 -0.756 1.00 0.00 A C 4 | ATOM 3 C3 NZADA 1 -5.475 8.576 -1.518 1.00 0.00 A C 5 | ATOM 4 C4 NZADA 1 -4.891 9.802 -1.350 1.00 0.00 A C 6 | ATOM 5 C5 NZADA 1 -5.185 10.514 -0.157 1.00 0.00 A C 7 | ATOM 6 C6 NZADA 1 -6.147 10.013 0.724 1.00 0.00 A C 8 | ATOM 7 H2 NZADA 1 -7.050 7.252 -1.090 1.00 0.00 A H 9 | ATOM 8 H3 NZADA 1 -5.156 7.920 -2.315 1.00 0.00 A H 10 | ATOM 9 H4 NZADA 1 -4.122 10.176 -2.010 1.00 0.00 A H 11 | ATOM 10 H5 NZADA 1 -4.597 11.322 0.252 1.00 0.00 A H 12 | ATOM 11 H6 NZADA 1 -6.339 10.420 1.706 1.00 0.00 A H 13 | ATOM 12 C7 NZADA 1 -8.034 8.561 1.361 1.00 0.00 A C 14 | ATOM 13 H71 NZADA 1 -8.926 8.161 0.834 1.00 0.00 A H 15 | ATOM 14 H72 NZADA 1 -8.421 9.441 1.917 1.00 0.00 A H 16 | ATOM 15 N8 NZADA 1 -7.534 7.601 2.287 1.00 0.00 A N 17 | ATOM 16 H8 NZADA 1 -6.825 7.052 1.851 1.00 0.00 A H 18 | ATOM 17 C9 NZADA 1 -7.389 7.834 3.608 1.00 0.00 A C 19 | ATOM 18 O9 NZADA 1 -7.809 8.797 4.247 1.00 0.00 A O 20 | ATOM 19 C10 NZADA 1 -6.798 6.680 4.365 1.00 0.00 A C 21 | ATOM 20 H101 NZADA 1 -6.883 6.926 5.445 0.00 0.00 A H 22 | ATOM 21 H102 NZADA 1 -5.723 6.689 4.083 0.00 0.00 A H 23 | ATOM 22 H103 NZADA 1 -7.123 5.631 4.193 0.00 0.00 A H 24 | END 25 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/n_methyl_acetamide.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 CL NMA A 1 -3.800 3.436 -4.188 0.00 0.00 A C 3 | ATOM 2 HL1 NMA A 1 -4.249 2.479 -4.523 0.00 0.00 A H 4 | ATOM 3 HL2 NMA A 1 -4.578 4.068 -3.715 0.00 0.00 A H 5 | ATOM 4 HL3 NMA A 1 -2.990 3.233 -3.459 0.00 0.00 A H 6 | ATOM 5 C NMA A 1 -3.225 4.163 -5.383 1.00 0.00 A C 7 | ATOM 6 O NMA A 1 -3.307 3.671 -6.479 1.00 0.00 A O 8 | ATOM 7 N NMA A 1 -2.654 5.324 -5.139 1.00 0.00 A N 9 | ATOM 8 H NMA A 1 -2.626 5.664 -4.206 0.00 0.00 A H 10 | ATOM 9 CR NMA A 1 -2.059 6.135 -6.182 0.00 0.00 A C 11 | ATOM 10 HR1 NMA A 1 -1.635 7.073 -5.757 0.00 0.00 A H 12 | ATOM 11 HR2 NMA A 1 -2.820 6.412 -6.946 0.00 0.00 A H 13 | ATOM 12 HR3 NMA A 1 -1.239 5.582 -6.691 0.00 0.00 A H 14 | END 15 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/octanol.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 C1 OCOHA 1 1.724 -4.002 8.878 1.00 0.00 A C 3 | ATOM 2 H11 OCOHA 1 2.130 -3.345 8.079 1.00 0.00 A H 4 | ATOM 3 H12 OCOHA 1 2.510 -4.754 9.103 1.00 0.00 A H 5 | ATOM 4 O1 OCOHA 1 1.670 -3.196 10.041 1.00 0.00 A O 6 | ATOM 5 HO1 OCOHA 1 0.881 -2.656 9.960 1.00 0.00 A H 7 | ATOM 6 C2 OCOHA 1 0.313 -4.591 8.668 1.00 0.00 A C 8 | ATOM 7 H21 OCOHA 1 -0.020 -5.092 9.603 1.00 0.00 A H 9 | ATOM 8 H22 OCOHA 1 0.537 -5.430 7.976 1.00 0.00 A H 10 | ATOM 9 C3 OCOHA 1 -0.778 -3.663 8.106 1.00 0.00 A C 11 | ATOM 10 H31 OCOHA 1 -1.086 -2.857 8.807 1.00 0.00 A H 12 | ATOM 11 H32 OCOHA 1 -1.657 -4.322 7.939 1.00 0.00 A H 13 | ATOM 12 C4 OCOHA 1 -0.334 -3.123 6.596 1.00 0.00 A C 14 | ATOM 13 H41 OCOHA 1 -1.080 -2.353 6.306 1.00 0.00 A H 15 | ATOM 14 H42 OCOHA 1 0.572 -2.495 6.733 1.00 0.00 A H 16 | ATOM 15 C5 OCOHA 1 0.053 -4.172 5.613 1.00 0.00 A C 17 | ATOM 16 H51 OCOHA 1 0.279 -3.676 4.646 1.00 0.00 A H 18 | ATOM 17 H52 OCOHA 1 1.015 -4.664 5.875 1.00 0.00 A H 19 | ATOM 18 C6 OCOHA 1 -1.137 -5.085 5.365 1.00 0.00 A C 20 | ATOM 19 H61 OCOHA 1 -1.994 -4.447 5.062 1.00 0.00 A H 21 | ATOM 20 H62 OCOHA 1 -1.310 -5.633 6.316 1.00 0.00 A H 22 | ATOM 21 C7 OCOHA 1 -0.847 -6.063 4.238 1.00 0.00 A C 23 | ATOM 22 H71 OCOHA 1 0.215 -6.384 4.178 1.00 0.00 A H 24 | ATOM 23 H72 OCOHA 1 -1.474 -6.964 4.407 1.00 0.00 A H 25 | ATOM 24 C8 OCOHA 1 -1.235 -5.477 2.919 1.00 0.00 A C 26 | ATOM 25 H81 OCOHA 1 -0.752 -6.041 2.092 1.00 0.00 A H 27 | ATOM 26 H82 OCOHA 1 -2.292 -5.585 2.595 1.00 0.00 A H 28 | ATOM 27 H83 OCOHA 1 -0.900 -4.435 2.733 1.00 0.00 A H 29 | END 30 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/oxindol_3_ylidene_rhodanine.pdb: -------------------------------------------------------------------------------- 1 | REMARK oxindol-3-ylidene rhodanine 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | ATOM 1 S1 OIRDA 1 -1.412 6.699 -1.863 1.00 0.00 A S 4 | ATOM 2 C2 OIRDA 1 -0.983 5.238 -2.660 1.00 0.00 A C 5 | ATOM 3 S2 OIRDA 1 0.369 5.014 -3.556 1.00 0.00 A S 6 | ATOM 4 N3 OIRDA 1 -1.887 4.256 -2.266 1.00 0.00 A N 7 | ATOM 5 H3 OIRDA 1 -1.884 3.356 -2.735 1.00 0.00 A H 8 | ATOM 6 C4 OIRDA 1 -2.907 4.565 -1.410 1.00 0.00 A C 9 | ATOM 7 O4 OIRDA 1 -3.762 3.749 -1.019 1.00 0.00 A O 10 | ATOM 8 C5 OIRDA 1 -2.887 6.016 -1.017 1.00 0.00 A C 11 | ATOM 9 C6 OIRDA 1 -3.795 6.637 -0.230 1.00 0.00 A C 12 | ATOM 10 C7 OIRDA 1 -3.706 8.150 -0.152 1.00 0.00 A C 13 | ATOM 11 O7 OIRDA 1 -2.824 8.924 -0.557 1.00 0.00 A O 14 | ATOM 12 N8 OIRDA 1 -4.720 8.580 0.558 1.00 0.00 A N 15 | ATOM 13 H8 OIRDA 1 -4.870 9.579 0.557 1.00 0.00 A H 16 | ATOM 14 C9 OIRDA 1 -5.489 7.576 1.060 1.00 0.00 A C 17 | ATOM 15 C10 OIRDA 1 -6.592 7.549 1.913 1.00 0.00 A C 18 | ATOM 16 H10 OIRDA 1 -7.073 8.478 2.179 1.00 0.00 A H 19 | ATOM 17 C11 OIRDA 1 -7.121 6.342 2.393 1.00 0.00 A C 20 | ATOM 18 H11 OIRDA 1 -8.037 6.316 2.964 1.00 0.00 A H 21 | ATOM 19 C12 OIRDA 1 -6.515 5.176 2.066 1.00 0.00 A C 22 | ATOM 20 H12 OIRDA 1 -6.932 4.282 2.507 1.00 0.00 A H 23 | ATOM 21 C13 OIRDA 1 -5.323 5.199 1.255 1.00 0.00 A C 24 | ATOM 22 H13 OIRDA 1 -4.842 4.272 0.980 1.00 0.00 A H 25 | ATOM 23 C14 OIRDA 1 -4.899 6.356 0.740 0.00 0.00 A C 26 | END 27 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/p_ethylphenol.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 CG EPHEA 1 -2.601 5.423 3.405 1.00 0.00 A C 3 | ATOM 2 CD1 EPHEA 1 -3.756 4.749 3.032 1.00 0.00 A C 4 | ATOM 3 HD1 EPHEA 1 -4.066 3.895 3.615 1.00 0.00 A H 5 | ATOM 4 CD2 EPHEA 1 -2.250 6.618 2.652 1.00 0.00 A C 6 | ATOM 5 HD2 EPHEA 1 -1.401 7.163 3.038 1.00 0.00 A H 7 | ATOM 6 CE1 EPHEA 1 -4.653 5.269 2.073 1.00 0.00 A C 8 | ATOM 7 HE1 EPHEA 1 -5.559 4.717 1.866 1.00 0.00 A H 9 | ATOM 8 CE2 EPHEA 1 -3.061 7.046 1.591 1.00 0.00 A C 10 | ATOM 9 HE2 EPHEA 1 -2.733 7.866 0.969 1.00 0.00 A H 11 | ATOM 10 CZ EPHEA 1 -4.287 6.388 1.338 1.00 0.00 A C 12 | ATOM 11 OH EPHEA 1 -5.218 6.809 0.385 1.00 0.00 A O 13 | ATOM 12 HH EPHEA 1 -6.028 6.371 0.657 1.00 0.00 A H 14 | ATOM 13 CB EPHEA 1 -1.727 4.926 4.527 1.00 0.00 A C 15 | ATOM 14 HB1 EPHEA 1 -2.133 4.014 5.016 1.00 0.00 A H 16 | ATOM 15 HB2 EPHEA 1 -0.722 4.756 4.087 1.00 0.00 A H 17 | ATOM 16 CA EPHEA 1 -1.672 5.937 5.686 1.00 0.00 A C 18 | ATOM 17 HA1 EPHEA 1 -1.586 6.967 5.280 1.00 0.00 A H 19 | ATOM 18 HA2 EPHEA 1 -0.634 5.770 6.044 1.00 0.00 A H 20 | ATOM 19 HA3 EPHEA 1 -2.462 5.738 6.441 1.00 0.00 A H 21 | END 22 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/phenol.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 CG PHENA 1 1.554 4.402 1.389 1.00 0.00 A C 3 | ATOM 2 HG PHENA 1 1.614 3.980 2.381 1.00 0.00 A H 4 | ATOM 3 CD1 PHENA 1 0.403 5.094 0.987 1.00 0.00 A C 5 | ATOM 4 HD1 PHENA 1 -0.424 5.205 1.672 1.00 0.00 A H 6 | ATOM 5 CD2 PHENA 1 2.630 4.255 0.502 1.00 0.00 A C 7 | ATOM 6 HD2 PHENA 1 3.518 3.722 0.810 1.00 0.00 A H 8 | ATOM 7 CE1 PHENA 1 0.329 5.641 -0.303 1.00 0.00 A C 9 | ATOM 8 HE1 PHENA 1 -0.560 6.173 -0.608 1.00 0.00 A H 10 | ATOM 9 CE2 PHENA 1 2.553 4.803 -0.787 1.00 0.00 A C 11 | ATOM 10 HE2 PHENA 1 3.378 4.695 -1.476 1.00 0.00 A H 12 | ATOM 11 CZ PHENA 1 1.405 5.494 -1.188 1.00 0.00 A C 13 | ATOM 12 OH PHENA 1 1.338 6.039 -2.484 1.00 0.00 A O 14 | ATOM 13 HH PHENA 1 0.483 6.469 -2.565 1.00 0.00 A H 15 | END 16 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/phenyl_sulfamate.pdb: -------------------------------------------------------------------------------- 1 | REMARK phenyl sulfamate 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | ATOM 1 S1 PMSTA 1 -1.853 4.371 -5.514 1.00 0.00 A S 4 | ATOM 2 C2 PMSTA 1 -0.698 5.725 -5.412 0.00 0.00 A C 5 | ATOM 3 H21 PMSTA 1 -0.586 6.208 -6.406 0.00 0.00 A H 6 | ATOM 4 H22 PMSTA 1 -1.099 6.431 -4.653 0.00 0.00 A H 7 | ATOM 5 H23 PMSTA 1 0.316 5.367 -5.132 0.00 0.00 A H 8 | ATOM 6 O11 PMSTA 1 -2.909 4.815 -6.341 1.00 0.00 A O 9 | ATOM 7 O12 PMSTA 1 -1.160 3.166 -5.895 1.00 0.00 A O 10 | ATOM 8 O3 PMSTA 1 -2.287 4.250 -4.005 1.00 0.00 A O 11 | ATOM 9 CZ PMSTA 1 -3.086 3.191 -3.674 1.00 0.00 A C 12 | ATOM 10 CE1 PMSTA 1 -2.447 1.997 -3.152 1.00 0.00 A C 13 | ATOM 11 HE1 PMSTA 1 -1.420 2.111 -2.838 1.00 0.00 A H 14 | ATOM 12 CE2 PMSTA 1 -4.446 3.073 -3.861 1.00 0.00 A C 15 | ATOM 13 HE2 PMSTA 1 -4.987 3.887 -4.321 1.00 0.00 A H 16 | ATOM 14 CD1 PMSTA 1 -3.084 0.809 -2.945 1.00 0.00 A C 17 | ATOM 15 HD1 PMSTA 1 -2.539 -0.103 -2.748 1.00 0.00 A H 18 | ATOM 16 CD2 PMSTA 1 -5.198 1.961 -3.536 1.00 0.00 A C 19 | ATOM 17 HD2 PMSTA 1 -6.215 1.826 -3.874 1.00 0.00 A H 20 | ATOM 18 CG PMSTA 1 -4.444 0.795 -3.158 1.00 0.00 A C 21 | ATOM 19 HG PMSTA 1 -4.988 -0.132 -3.050 1.00 0.00 A H 22 | END 23 | -------------------------------------------------------------------------------- /BUILD_DIR/SmallMolecules/propionic_acid.pdb: -------------------------------------------------------------------------------- 1 | COMPND Propionic acid 2 | AUTHOR GENERATED BY OPEN BABEL 2.3.90 3 | HETATM 1 C1 PROA 1 1.657 2.600 -0.017 1.00 0.00 C 4 | HETATM 2 C2 PROA 1 1.126 1.246 -0.484 1.00 0.00 C 5 | HETATM 3 C3 PROA 1 1.591 0.163 0.469 1.00 0.00 C 6 | HETATM 4 H21 PROA 1 1.494 1.046 -1.496 1.00 0.00 H 7 | HETATM 5 H22 PROA 1 0.032 1.261 -0.528 1.00 0.00 H 8 | HETATM 6 H31 PROA 1 2.683 0.088 0.488 1.00 0.00 H 9 | HETATM 7 H32 PROA 1 1.191 -0.809 0.162 1.00 0.00 H 10 | HETATM 8 H33 PROA 1 1.251 0.365 1.490 1.00 0.00 H 11 | HETATM 9 O1 PROA 1 2.907 2.753 -0.115 1.00 0.00 O 12 | HETATM 10 O2 PROA 1 0.775 3.405 0.395 1.00 0.00 O 13 | CONECT 1 2 9 10 14 | CONECT 2 1 3 4 5 15 | CONECT 3 2 6 7 8 16 | CONECT 4 2 17 | CONECT 5 2 18 | CONECT 6 3 19 | CONECT 7 3 20 | CONECT 8 3 21 | CONECT 9 1 22 | CONECT 10 1 23 | MASTER 0 0 0 0 0 0 0 0 10 0 10 0 24 | END 25 | -------------------------------------------------------------------------------- /BUILD_DIR/build_example: -------------------------------------------------------------------------------- 1 | # VMD psfgen example: 2 | # this script generates a psf and pdb file of a given 3 | # structure in preparation of a namd simulation. 4 | # 5 | # 6 | # usage: at the command line type: 7 | # vmd -dispdev text -e build_example 8 | 9 | package require psfgen 10 | 11 | #topology ../InputFiles/Parameters/top_all27_prot_na.rtf 12 | 13 | topology ../InputFiles/Parameters/top_all36_prot.rtf 14 | topology ../InputFiles/Parameters/top_all36_na.rtf 15 | topology ../InputFiles/Parameters/top_all36_lipid.rtf 16 | topology ../InputFiles/Parameters/top_all36_carb.rtf 17 | topology ../InputFiles/Parameters/toppar_water_ions_namd.str 18 | 19 | 20 | # 21 | # Alias residue names 22 | alias residue HIS HSE 23 | alias atom ILE CD1 CD 24 | 25 | # Build protein segment 26 | 27 | segment A {pdb ../Examples/1ubq_chainA.pdb} 28 | 29 | # Patch protein segment: for adding disulphide bonds etc: segment MF {pdb nad.pdb} 30 | 31 | # patch DISU A:97 A:104 32 | # patch TP2 A:199 33 | # regenerate angles dihedrals 34 | 35 | coordpdb ../Examples/1ubq_chainA.pdb A 36 | 37 | guesscoord 38 | 39 | # Write structure and coordinate files 40 | 41 | writepsf model_temp_x.psf 42 | writepdb model_temp_x.pdb 43 | 44 | # Still need to solvate and ionize! 45 | # do that with vmd modules 46 | 47 | exit 48 | -------------------------------------------------------------------------------- /BUILD_DIR/build_notes.txt: -------------------------------------------------------------------------------- 1 | Model building notes. 2 | 3 | Checklist: 4 | 5 | -------------------------------------------------------------------------------- /BUILD_DIR/hexagonal_solvate.vmd: -------------------------------------------------------------------------------- 1 | # VMD for LINUXAMD64, version 1.9.4a38 (October 17, 2019) 2 | # Hexagonal periodic boundary conditions script. mk July 2020 3 | 4 | # This script is designed to help solvate with hexagonal boundary conditions. 5 | 6 | # Hexagonal boundary condition can be tricky to set up. 7 | # From the top it looks like this: 8 | 9 | # . __________ _ 10 | # / | / | 11 | # / |/ | Y 12 | # /| / | 13 | # /_|______/. _| 14 | # 15 | # |---X---| 16 | # which should also have a depth Z. 17 | 18 | # The easiest way I've found is to is simply solvate & ionize rectangular box with VMD such that 19 | # Y = sqrt(3)*X/2 20 | 21 | # Then thouroughly minimize with a script which has hexagonal axis enabled. (10,000 steps) 22 | # as the X/Y dimensions should be correct, the minimization should wrap the corners to 23 | # the appropriate sides to make the appropriate hexagonal shape. 24 | 25 | #ie) 26 | # Periodic Boundary Conditions: ---------------------------------------------- 27 | ## make sure to check that the cell dimensions match your input files! 28 | # cellBasisVector1 160. 0. 0. 29 | # cellBasisVector2 80. 138.564 0. 30 | # cellBasisVector3 0. 0. 250. 31 | # cellOrigin 0 0 0 32 | # wrapAll on 33 | # wrapWater on 34 | # 35 | ## for hexagonal PBC: 36 | ## v1 ( r 0 0 ) 37 | ## v2 ( r/2 3*0.5*r/2 0 ) 38 | ## v3 ( 0 0 h ) 39 | # 40 | 41 | package require solvate 42 | set X 85 43 | set Z 150 44 | set Y [format %.5f [expr 3**0.5 * $X / 2] ] 45 | 46 | set a "{-$X -$Y -$Z}" 47 | set b "{ $X $Y $Z}" 48 | 49 | #solvate model_temp_x.psf model_temp_x.pdb -o solvate -s WT -b 1.8 -minmax {{-80 -69.28203 -150} {80 69.28203 150}} 50 | #package require autoionize 51 | #autoionize -psf solvate.psf -pdb solvate.pdb -sc 0.15 52 | # 53 | #mol new {ionized.psf} type {psf} first 0 last -1 step 1 waitfor 1 54 | #mol new {ionized.pdb} type {pdb} first 0 last -1 step 1 waitfor 1 55 | 56 | exit 57 | 58 | -------------------------------------------------------------------------------- /BUILD_DIR/molecule_prep_helper1.vmd: -------------------------------------------------------------------------------- 1 | # VMD for LINUXAMD64, version 1.9.4a38 (October 17, 2019) 2 | # Log file '/scratch1/kui00b/MOLECULES_2018/BUILD_DIR/molecule_prep2.vmd', created by user kui00b 3 | menu files off 4 | menu files on 5 | mol addrep 0 6 | display resetview 7 | mol new {ionized.psf} type {psf} first 0 last -1 step 1 waitfor 1 8 | animate style Loop 9 | display resetview 10 | mol addfile {ionized.pdb} type {pdb} first 0 last -1 step 1 waitfor 1 0 11 | animate style Loop 12 | mol addfile {opt_01.dcd} type {dcd} first 0 last -1 step 1 waitfor 1 0 13 | animate style Loop 14 | menu save off 15 | menu save on 16 | set sel0 [atomselect top all] 17 | $sel0 set beta 0.0 18 | set sel [atomselect top all frame last] 19 | $sel writepdb ionized.pdb 20 | 21 | exit 22 | # VMD for LINUXAMD64, version 1.9.4a38 (October 17, 2019) 23 | # end of log file. 24 | 25 | -------------------------------------------------------------------------------- /BUILD_DIR/optimization_01.coor: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/BUILD_DIR/optimization_01.coor -------------------------------------------------------------------------------- /BUILD_DIR/optimization_01.dcd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/BUILD_DIR/optimization_01.dcd -------------------------------------------------------------------------------- /BUILD_DIR/optimization_01.restart.coor: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/BUILD_DIR/optimization_01.restart.coor -------------------------------------------------------------------------------- /BUILD_DIR/optimization_01.restart.vel: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/BUILD_DIR/optimization_01.restart.vel -------------------------------------------------------------------------------- /BUILD_DIR/optimization_01.restart.xsc: -------------------------------------------------------------------------------- 1 | # NAMD extended system configuration restart file 2 | #$LABELS step o_x o_y o_z 3 | 5000 0 0 0 4 | -------------------------------------------------------------------------------- /BUILD_DIR/optimization_01.vel: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/BUILD_DIR/optimization_01.vel -------------------------------------------------------------------------------- /BUILD_DIR/optimization_01.xsc: -------------------------------------------------------------------------------- 1 | # NAMD extended system configuration output file 2 | #$LABELS step o_x o_y o_z 3 | 6000 0 0 0 4 | -------------------------------------------------------------------------------- /BUILD_DIR/optimization_01.xst: -------------------------------------------------------------------------------- 1 | # NAMD extended system trajectory file 2 | #$LABELS step o_x o_y o_z 3 | 0 0 0 0 4 | 500 0 0 0 5 | 1000 0 0 0 6 | 1000 0 0 0 7 | 1500 0 0 0 8 | 2000 0 0 0 9 | 2500 0 0 0 10 | 3000 0 0 0 11 | 3500 0 0 0 12 | 4000 0 0 0 13 | 4500 0 0 0 14 | 5000 0 0 0 15 | 5500 0 0 0 16 | 6000 0 0 0 17 | -------------------------------------------------------------------------------- /BUILD_DIR/packmol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/BUILD_DIR/packmol -------------------------------------------------------------------------------- /BUILD_DIR/packmol_config_file.cfg: -------------------------------------------------------------------------------- 1 | # 2 | # a mixture of metabolites 3 | # 4 | 5 | # All the atoms from different molecules will be separated at least 2.0 6 | # Angstroms at the solution. 7 | # usage: packmol < packmol_config_file.cfg 8 | 9 | tolerance 4.0 10 | 11 | # The file type of input and output files is PDB 12 | 13 | filetype pdb 14 | 15 | # The name of the output file 16 | 17 | output mixture.pdb 18 | 19 | # 20 | 21 | structure 6lu7_chainA.pdb 22 | number 1 23 | fixed 0. 0. 0. 0. 0. 0 24 | end structure 25 | 26 | structure 6lu7_chainB.pdb 27 | number 1 28 | fixed 0. 0. 0. 0. 0. 0 29 | end structure 30 | 31 | structure AminoAcids/ala.pdb 32 | number 4 33 | inside box -40 -40 -40 40 40 40 34 | end structure 35 | 36 | structure AminoAcids/cys.pdb 37 | number 4 38 | inside box -40 -40 -40 40 40 40 39 | end structure 40 | 41 | structure AminoAcids/asp.pdb 42 | number 4 43 | inside box -40 -40 -40 40 40 40 44 | end structure 45 | 46 | structure AminoAcids/glu.pdb 47 | number 4 48 | inside box -40 -40 -40 40 40 40 49 | end structure 50 | 51 | structure AminoAcids/phe.pdb 52 | number 4 53 | inside box -40 -40 -40 40 40 40 54 | end structure 55 | 56 | #structure AminoAcids/gly.pdb 57 | # number 4 58 | # inside box -40 -40 -40 40 40 40 59 | #end structure 60 | 61 | structure AminoAcids/his.pdb 62 | number 4 63 | inside box -40 -40 -40 40 40 40 64 | end structure 65 | 66 | structure AminoAcids/ile.pdb 67 | number 4 68 | inside box -40 -40 -40 40 40 40 69 | end structure 70 | 71 | structure AminoAcids/lys.pdb 72 | number 4 73 | inside box -40 -40 -40 40 40 40 74 | end structure 75 | 76 | structure AminoAcids/leu.pdb 77 | number 4 78 | inside box -40 -40 -40 40 40 40 79 | end structure 80 | 81 | structure AminoAcids/met.pdb 82 | number 4 83 | inside box -40 -40 -40 40 40 40 84 | end structure 85 | 86 | structure AminoAcids/asn.pdb 87 | number 4 88 | inside box -40 -40 -40 40 40 40 89 | end structure 90 | 91 | #structure AminoAcids/pro.pdb 92 | # number 4 93 | # inside box -40 -40 -40 40 40 40 94 | #end structure 95 | 96 | structure AminoAcids/gln.pdb 97 | number 4 98 | inside box -40 -40 -40 40 40 40 99 | end structure 100 | 101 | structure AminoAcids/arg.pdb 102 | number 4 103 | inside box -40 -40 -40 40 40 40 104 | end structure 105 | 106 | structure AminoAcids/ser.pdb 107 | number 4 108 | inside box -40 -40 -40 40 40 40 109 | end structure 110 | 111 | structure AminoAcids/thr.pdb 112 | number 4 113 | inside box -40 -40 -40 40 40 40 114 | end structure 115 | 116 | structure AminoAcids/val.pdb 117 | number 4 118 | inside box -40 -40 -40 40 40 40 119 | end structure 120 | 121 | structure AminoAcids/trp.pdb 122 | number 4 123 | inside box -40 -40 -40 40 40 40 124 | end structure 125 | 126 | structure AminoAcids/tyr.pdb 127 | number 4 128 | inside box -40 -40 -40 40 40 40 129 | end structure 130 | 131 | 132 | -------------------------------------------------------------------------------- /BUILD_DIR/solvate_ionize_script.vmd: -------------------------------------------------------------------------------- 1 | # VMD for LINUXAMD64, version 1.9.4a38 (October 17, 2019) 2 | # Hexagonal periodic boundary conditions script. mk July 2020 3 | 4 | # This script is designed to help solvate with hexagonal boundary conditions. 5 | 6 | # Hexagonal boundary condition can be tricky to set up. 7 | # From the top it looks like this: 8 | 9 | # . __________ _ 10 | # / | / | 11 | # / |/ | Y 12 | # /| / | 13 | # /_|______/. _| 14 | # 15 | # |---X---| 16 | # which should also have a depth Z. 17 | 18 | # The easiest way I've found is to is simply solvate & ionize rectangular box with VMD such that 19 | # Y = sqrt(3)*X/2 20 | 21 | # Then thouroughly minimize with a script which has hexagonal axis enabled. (10,000 steps) 22 | # as the X/Y dimensions should be correct, the minimization should wrap the corners to 23 | # the appropriate sides to make the appropriate hexagonal shape. 24 | 25 | #ie) 26 | # Periodic Boundary Conditions: ---------------------------------------------- 27 | ## make sure to check that the cell dimensions match your input files! 28 | # cellBasisVector1 160. 0. 0. 29 | # cellBasisVector2 80. 138.564 0. 30 | # cellBasisVector3 0. 0. 250. 31 | # cellOrigin 0 0 0 32 | # wrapAll on 33 | # wrapWater on 34 | # 35 | ## for hexagonal PBC: 36 | ## v1 ( r 0 0 ) 37 | ## v2 ( r/2 3*0.5*r/2 0 ) 38 | ## v3 ( 0 0 h ) 39 | # 40 | 41 | package require solvate 42 | set X 65 43 | set Z 150 44 | set Y [format %.5f [expr 3**0.5 * $X / 2] ] 45 | 46 | # set a "{-$X -$Y -$Z}" 47 | # set b "{ $X $Y $Z}" 48 | 49 | solvate model_temp_x.psf model_temp_x.pdb -o solvate -s WT -b 1.8 -minmax {{-32 -32 -36} {32 32 36}} 50 | #solvate model_temp_x.psf model_temp_x.pdb -o solvate1 -s WA -b 1.8 -minmax {{-60 -60 15} {60 60 70}} 51 | #solvate solvate1.psf solvate1.pdb -o solvate -s WB -b 1.8 -minmax {{-60 -60 -70} {60 60 -15}} 52 | 53 | package require autoionize 54 | autoionize -psf solvate.psf -pdb solvate.pdb -sc 0.15 -cation POT 55 | #autoionize -psf ionized.psf -pdb ionized.pdb -nions {{CAL 10} {CLA 20}} 56 | # 57 | mol new {ionized.psf} type {psf} first 0 last -1 step 1 waitfor 1 58 | mol new {ionized.pdb} type {pdb} first 0 last -1 step 1 waitfor 1 59 | 60 | # to set CA atomse of protein and ligand to 1.0 for constraints while optimizing. 61 | set sel2 [atomselect top {protein and name CA}] 62 | $sel2 set beta 1.0 63 | set sel [atomselect top all] 64 | $sel writepdb ionized.pdb 65 | 66 | exit 67 | 68 | -------------------------------------------------------------------------------- /Examples/create_local_dcd_loader_script: -------------------------------------------------------------------------------- 1 | #! /bin/bash 2 | # mk Jan 2013 3 | # This script is used to generate a setup local vmd script that can conveniently 4 | # load in all production dcd files listed in this current directory. 5 | # Typically one would run this from the local job directory 6 | 7 | # 8 | 9 | 10 | # Can edit the following variables to select the input frames: 11 | 12 | first_frame=0 13 | last_frame=-1 14 | step_size=1 15 | 16 | 17 | # Assuming script runs in /MainJob_dir/Jobxxx 18 | # grab local directory name: 19 | 20 | # cdir=`pwd` 21 | # jobdir=`basename $cdir` 22 | basename=local_dcd_file_loader 23 | 24 | # 25 | # cd OutputFiles 26 | 27 | # - create dcd list from exisiting dcd files 28 | ls *.dcd > dcd_list.txt 29 | 30 | # create local dcd list for vmd setup file: 31 | echo "" >$basename.vmd 32 | 33 | for dcdline in $(cat dcd_list.txt); 34 | do 35 | printf "mol addfile OutputFiles/%s type dcd first %s last %s step %s filebonds 1 autobonds 1 waitfor all\n" $dcdline $first_frame $last_frame $step_size >>$basename.vmd 36 | done 37 | 38 | #-- cleanup: 39 | if [ -f dcd_list.txt ]; 40 | then 41 | rm dcd_list.txt 42 | fi 43 | 44 | cd ../ 45 | 46 | -------------------------------------------------------------------------------- /Examples/master_config_file: -------------------------------------------------------------------------------- 1 | { 2 | "Comment0" : "Master_Config_File v0.1", 3 | "Account" : "VR0000", 4 | 5 | "Comment1" : "BlueGene/Q Namd Job parameters:", 6 | "nodes" : "2", 7 | "ntpn" : "8", 8 | "ppn" : "8", 9 | "Walltime" : "24:0:0", 10 | "ModuleFile" : "namd-xl-pami-smp/2.9", 11 | "PsfFileName" : "ChangeMe.psf", 12 | "PdbFileName" : "ChangeMe.pdb", 13 | 14 | "Comment2" : "Job Setup Dimensions", 15 | "SimReplicates": "4", 16 | "Runs" : "10", 17 | "JobScheme" : "simple", 18 | "Round" : "1", 19 | 20 | "Comment3" : "Job Input Details", 21 | "JobDir" : "Main_Job_Dir", 22 | "BaseDirName" : "My_Sim_", 23 | 24 | "OptJobName" : "optimization_job_", 25 | "SbatchStartScript" : "sbatch_start.template", 26 | "OptimizeConfScript": "sim_opt.conf", 27 | 28 | "ProductionJobName" : "production_job_", 29 | "SbatchProdScript" : "sbatch_production.template", 30 | "ProdConfScript" : "sim_production.conf", 31 | 32 | "custom_script1" : "custom1.conf", 33 | "custom_script2" : "custom2.conf", 34 | 35 | "Comment4" : "Miscelaneous Parameters", 36 | "JobFailTime" : "300", 37 | "DiskSpaceCutOff": "95" 38 | 39 | } 40 | 41 | -------------------------------------------------------------------------------- /Examples/readme.txt: -------------------------------------------------------------------------------- 1 | # Examples directory. 2 | # 3 | # Some example files for running jobs. 4 | 5 | -------------------------------------------------------------------------------- /InputFiles/Parameters/ace/acepar19.inp: -------------------------------------------------------------------------------- 1 | * ACE2 parameter file (under construction, Jan 2002) 2 | * >>>> for use with param19 <<<< 3 | * Author: Michael Schaefer ! (schaefer@piaf.u-strasbg.fr) 4 | * Reserved (4-letter) keywords: VOLU, SIGM, A012, RMIN, EQUI, END. 5 | * The file MUST end with the END keyword. 6 | * 7 | 8 | VOLUMES 9 | ! Effective Voronoi atom volumes, use with smoothing parameter alpha=1.3 10 | ! Reference: M. Schaefer, C. Bartels, F. Leclerc, and M. Karplus, 11 | ! J. Comp. Chem. 22 (2001), 1857-1879. 12 | H 0.0000 13 | HC 0.0000 14 | C 8.8950 15 | CH1E 12.4300 16 | CH2E 22.0330 17 | CH3E 34.0920 18 | CR1E 20.9790 19 | N 9.5580 20 | NR 16.5900 21 | NP 11.4950 22 | NH1 14.9440 23 | NH2 22.1290 24 | NH3 20.6410 25 | NC2 21.4010 26 | NH2P 16.3050 27 | O 22.3150 28 | OC 20.4850 29 | OH1 23.2660 30 | S 26.9630 31 | SH1E 34.1920 32 | SSO4 5.0260 33 | FE 10.7030 34 | 35 | END 36 | -------------------------------------------------------------------------------- /InputFiles/Parameters/ace/acepar22_prot.inp: -------------------------------------------------------------------------------- 1 | * ACE2 parameter file (under construction, Jan 2002) 2 | * >>>> for use with par_all22_prot <<<< 3 | * Author: Michael Schaefer ! (schaefer@piaf.u-strasbg.fr) 4 | * Reserved (4-letter) keywords: VOLU, SIGM, A012, RMIN, EQUI, END. 5 | * The file MUST end with the END keyword. 6 | * 7 | 8 | VOLUMES 9 | ! Effective Voronoi atom volumes, use with smoothing parameter alpha=1.3 10 | ! Reference: M. Schaefer, C. Bartels, F. Leclerc, and M. Karplus, 11 | ! J. Comp. Chem. 22 (2001), 1857-1879. 12 | H 0.0000 13 | HC 0.0000 14 | HA 0.0000 15 | HP 0.0000 16 | HB 0.0000 17 | HR1 0.0000 18 | HR3 0.0000 19 | HS 0.0000 20 | HT 0.0000 ! TIP3 21 | C 8.5590 22 | CA 21.2450 23 | CT1 12.3350 24 | CT2 21.9090 25 | CT3 34.1160 26 | CPH1 15.2480 27 | CPH2 17.8930 28 | CPT 10.4070 29 | CY 10.5050 30 | CP1 12.9160 31 | CP2 24.3960 32 | CP3 22.3300 33 | CC 9.2150 34 | CPA 10.7540 35 | CPB 11.1880 36 | CPM 19.9980 37 | CA3 10.2130 38 | N 9.4180 39 | NR1 18.0190 40 | NR2 17.8970 41 | NH1 14.7980 42 | NH2 25.0010 43 | NH3 24.5440 44 | NC2 24.5090 45 | NY 18.8470 46 | NP 17.6250 47 | NPH 11.5350 48 | NC2E 17.2860 49 | O 22.7090 50 | OC 21.6170 51 | OH1 24.4730 52 | OT 23.1570 ! TIP3, OT van der Waals volume 53 | S 29.8490 54 | SM 26.3250 55 | SSO4 5.0260 ! SO4 sulfate S volume, from results on param19 56 | FE 10.4580 57 | 58 | END 59 | -------------------------------------------------------------------------------- /InputFiles/Parameters/ace/acepar27_na.inp: -------------------------------------------------------------------------------- 1 | * ACE2 parameter file (under construction, Jan 2002) 2 | * >>>> for use with par_all27_na <<<< 3 | * Author: Michael Schaefer ! (schaefer@piaf.u-strasbg.fr) 4 | * Reserved (4-letter) keywords: VOLU, SIGM, A012, RMIN, EQUI, END. 5 | * The file MUST end with the END keyword. 6 | * 7 | 8 | VOLUMES 9 | ! Effective Voronoi atom volumes, use with smoothing parameter alpha=1.1 10 | ! Reference: M. Schaefer, C. Bartels, F. Leclerc, and M. Karplus, 11 | ! J. Comp. Chem. 22 (2001), 1857-1879. 12 | HN1 0.0000 13 | HN2 0.0000 14 | HN3 0.0000 15 | HN5 0.0000 16 | HN7 0.0000 17 | HN8 0.0000 18 | HN9 0.0000 19 | CN1 8.3670 20 | CN1T 8.4060 21 | CN2 8.5500 22 | CN3 17.3170 23 | CN3T 9.8890 24 | CN4 17.1250 25 | CN5 8.9150 26 | CN5G 9.1600 27 | CN7 12.7100 28 | CN7B 12.2210 29 | CN8 20.2050 30 | CN8B 20.6310 31 | CN9 30.7750 32 | NN1 21.7910 33 | NN2 9.2230 34 | NN2B 9.2630 35 | NN2U 14.2200 36 | NN2G 14.0690 37 | NN3 13.9170 38 | NN3A 14.1390 39 | NN3G 16.3950 40 | NN4 16.7840 41 | NN3B 16.9620 42 | ON1 20.2730 43 | ON1C 20.3190 44 | ON2 15.7230 45 | ON3 19.4700 46 | ON5 20.8370 47 | ON6 16.4680 48 | ON6B 15.8860 49 | P 6.2230 50 | MG 7.0000 51 | SOD 10.6241 ! van der Waals volume 52 | 53 | END 54 | -------------------------------------------------------------------------------- /InputFiles/Parameters/alanine.str: -------------------------------------------------------------------------------- 1 | * Toppar stream file generated by 2 | * CHARMM General Force Field (CGenFF) program version 1.0.0 3 | * For use with CGenFF version 3.0.1 4 | * 5 | 6 | read rtf card append 7 | * Topologies generated by 8 | * CHARMM General Force Field (CGenFF) program version 1.0.0 9 | * 10 | 36 1 11 | 12 | ! "penalty" is the highest penalty score of the associated parameters. 13 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 14 | ! and 50 mean some basic validation is recommended; penalties higher than 15 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 16 | 17 | RESI ALAX 0.000 ! param penalty= 0.000 ; charge penalty= 102.874 18 | GROUP ! CHARGE CH_PENALTY 19 | ATOM HA HGA1 0.090 ! 4.013 20 | ATOM CA CG314 0.348 ! 102.874 21 | ATOM N NG3P3 -0.348 ! 37.442 22 | ATOM H1 HGP2 0.330 ! 2.536 23 | ATOM H2 HGP2 0.330 ! 2.536 24 | ATOM CB CG331 -0.275 ! 31.175 25 | ATOM HB1 HGA3 0.090 ! 2.536 26 | ATOM HB2 HGA3 0.090 ! 2.536 27 | ATOM HB3 HGA3 0.090 ! 2.536 28 | ATOM C CG2O3 0.445 ! 99.992 29 | ATOM O OG2D2 -0.760 ! 8.256 30 | ATOM OXT OG2D2 -0.760 ! 8.256 31 | ATOM H3 HGP2 0.330 ! 2.536 32 | 33 | BOND HA CA 34 | BOND CA N 35 | BOND CA CB 36 | BOND CA C 37 | BOND N H1 38 | BOND N H2 39 | BOND CB HB1 40 | BOND CB HB2 41 | BOND CB HB3 42 | BOND C O 43 | BOND C OXT 44 | BOND H3 N 45 | IMPR C OXT O CA 46 | 47 | END 48 | 49 | read param card flex append 50 | * Parameters generated by analogy by 51 | * CHARMM General Force Field (CGenFF) program version 1.0.0 52 | * 53 | 54 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 55 | ! and 50 mean some basic validation is recommended; penalties higher than 56 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 57 | 58 | BONDS 59 | 60 | ANGLES 61 | 62 | DIHEDRALS 63 | 64 | IMPROPERS 65 | 66 | END 67 | RETURN 68 | -------------------------------------------------------------------------------- /InputFiles/Parameters/aspartate.str: -------------------------------------------------------------------------------- 1 | * Toppar stream file generated by 2 | * CHARMM General Force Field (CGenFF) program version 1.0.0 3 | * For use with CGenFF version 3.0.1 4 | * 5 | 6 | read rtf card append 7 | * Topologies generated by 8 | * CHARMM General Force Field (CGenFF) program version 1.0.0 9 | * 10 | 36 1 11 | 12 | ! "penalty" is the highest penalty score of the associated parameters. 13 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 14 | ! and 50 mean some basic validation is recommended; penalties higher than 15 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 16 | 17 | RESI ASPX -1.000 ! param penalty= 0.000 ; charge penalty= 108.292 18 | GROUP ! CHARGE CH_PENALTY 19 | ATOM HA HGA1 0.090 ! 4.621 20 | ATOM CA CG314 0.367 ! 108.292 21 | ATOM C CG2O3 0.445 ! 99.918 22 | ATOM O OG2D2 -0.760 ! 8.256 23 | ATOM OXT OG2D2 -0.760 ! 8.256 24 | ATOM CB CG321 -0.255 ! 46.872 25 | ATOM CG CG2O3 0.587 ! 12.353 26 | ATOM HB1 HGA2 0.090 ! 2.500 27 | ATOM N NG3P3 -0.364 ! 41.116 28 | ATOM H1 HGP2 0.330 ! 2.536 29 | ATOM H2 HGP2 0.330 ! 2.536 30 | ATOM OD1 OG2D2 -0.760 ! 0.850 31 | ATOM OD2 OG2D2 -0.760 ! 0.850 32 | ATOM HB2 HGA2 0.090 ! 2.500 33 | ATOM H3 HGP2 0.330 ! 2.536 34 | 35 | BOND HA CA 36 | BOND CA C 37 | BOND CA CB 38 | BOND CA N 39 | BOND C O 40 | BOND C OXT 41 | BOND CB HB1 42 | BOND N H1 43 | BOND N H2 44 | BOND CB CG 45 | BOND CG OD1 46 | BOND CG OD2 47 | BOND CB HB2 48 | BOND H3 N 49 | IMPR C OXT O CA 50 | IMPR CG OD2 OD1 CB 51 | 52 | END 53 | 54 | read param card flex append 55 | * Parameters generated by analogy by 56 | * CHARMM General Force Field (CGenFF) program version 1.0.0 57 | * 58 | 59 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 60 | ! and 50 mean some basic validation is recommended; penalties higher than 61 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 62 | 63 | BONDS 64 | 65 | ANGLES 66 | 67 | DIHEDRALS 68 | 69 | IMPROPERS 70 | 71 | END 72 | RETURN 73 | -------------------------------------------------------------------------------- /InputFiles/Parameters/drude/drude_toppar_2019.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/InputFiles/Parameters/drude/drude_toppar_2019.tgz -------------------------------------------------------------------------------- /InputFiles/Parameters/drude/positive_drude.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/InputFiles/Parameters/drude/positive_drude.tgz -------------------------------------------------------------------------------- /InputFiles/Parameters/drude/toppar_defs_2019.str: -------------------------------------------------------------------------------- 1 | * stream drude toppar files 2 | * 3 | 4 | stream @toppar/toppar_drude_master_protein_2019g.str 5 | stream @toppar/toppar_drude_d_aminoacids_2019g.str 6 | stream @toppar/toppar_drude_carbohydrate_2019a.str 7 | stream @toppar/toppar_drude_nucleic_acid_2017c.str 8 | stream @toppar/toppar_drude_lipid_2017c.str 9 | stream @toppar/toppar_drude_model_2019g.str 10 | 11 | return 12 | -------------------------------------------------------------------------------- /InputFiles/Parameters/gbsw/00readme: -------------------------------------------------------------------------------- 1 | 2 | Files yet to be tested with c36 protein parameters 3 | -------------------------------------------------------------------------------- /InputFiles/Parameters/gbsw/radius_gbsw.str: -------------------------------------------------------------------------------- 1 | * PMF guided optimization of input radii for charged residues 2 | * J. Chen, W. Im and C. L. Brooks III, JACS (submitted) 3 | * NOTE: should be used only with GBSW; 4 | * NOTE: for optimal accuracy in peptide and protein conformational equilibrium, 5 | * the modified CMAP in "~toppar/gbsw/par_all22_prot_gbsw.inp" should be used. 6 | * 7 | 8 | ! ASP and GLU (no change) 9 | 10 | ! LYS: 11 | scalar wmain set 1.8 select resn LYS .and. type NZ end 12 | 13 | ! ARG: 14 | scalar wmain set 1.7 select resn ARG .and. ( type NH* .or. type NE ) end 15 | scalar wmain set 2.2 select resn ARG .and. type CZ end 16 | 17 | ! GLN and ASN 18 | scalar wmain set 1.6 select resn GLN .and. type OE1 end 19 | scalar wmain set 1.6 select resn ASN .and. type OD1 end 20 | scalar wmain set 2.0 select resn GLN .and. type NE2 end 21 | scalar wmain set 2.0 select resn ASN .and. type ND2 end 22 | 23 | ! HSD and HSP: hnd(1.8->1.9), hpnd/hpne(2.3->1.9) 24 | scalar wmain set 1.9 select resn HSD .and. type ND1 end 25 | scalar wmain set 1.9 select resn HSP .and. type ND1 end 26 | scalar wmain set 1.9 select resn HSP .and. type NE2 end 27 | 28 | ! TRP: NE (2.4->1.8), C*(1.78->2.0) 29 | scalar wmain set 1.85 select resn TRP .and. type NE1 end 30 | scalar wmain set 2.0 select resn TRP - 31 | .and. (type CE* .or. type CD* .or. type CZ* .or. type CH2) end 32 | 33 | ! backbone (bb6) 34 | scalar wmain set 2.03 sele type N end !2.23 35 | scalar wmain set 2.03 sele type NL .or. type NR end ! alad 36 | 37 | ! terminus 38 | scalar wmain set 2.03 sele type NT end ! 2.23 39 | scalar wmain set 2.77 sele type CGY end ! from GLU CG 40 | scalar wmain set 2.67 sele type CAY end ! from CB 41 | scalar wmain set 1.98 sele type CDY end ! from GLU CD 42 | scalar wmain set 1.40 sele type OEY* end ! from GLU OE* 43 | scalar wmain set 1.52 sele type OY end ! from backbone O 44 | scalar wmain set 2.04 sele type CY endi ! from backbone C 45 | -------------------------------------------------------------------------------- /InputFiles/Parameters/glutamate.str: -------------------------------------------------------------------------------- 1 | * Toppar stream file generated by 2 | * CHARMM General Force Field (CGenFF) program version 1.0.0 3 | * For use with CGenFF version 3.0.1 4 | * 5 | 6 | read rtf card append 7 | * Topologies generated by 8 | * CHARMM General Force Field (CGenFF) program version 1.0.0 9 | * 10 | 36 1 11 | 12 | ! "penalty" is the highest penalty score of the associated parameters. 13 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 14 | ! and 50 mean some basic validation is recommended; penalties higher than 15 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 16 | 17 | RESI GLXU -1.000 ! param penalty= 0.000 ; charge penalty= 102.808 18 | GROUP ! CHARGE CH_PENALTY 19 | ATOM C CG2O3 0.445 ! 99.918 20 | ATOM CA CG314 0.340 ! 102.808 21 | ATOM N NG3P3 -0.362 ! 37.436 22 | ATOM CB CG321 -0.178 ! 31.642 23 | ATOM HB1 HGA2 0.090 ! 2.500 24 | ATOM HB2 HGA2 0.090 ! 2.500 25 | ATOM CG CG321 -0.267 ! 9.641 26 | ATOM HG1 HGA2 0.090 ! 0.000 27 | ATOM HG2 HGA2 0.090 ! 0.000 28 | ATOM CD CG2O3 0.622 ! 9.528 29 | ATOM OE1 OG2D2 -0.760 ! 0.000 30 | ATOM OE2 OG2D2 -0.760 ! 0.000 31 | ATOM O OG2D2 -0.760 ! 8.256 32 | ATOM OXT OG2D2 -0.760 ! 8.256 33 | ATOM HA HGA1 0.090 ! 3.979 34 | ATOM H1 HGP2 0.330 ! 2.536 35 | ATOM H2 HGP2 0.330 ! 2.536 36 | ATOM H3 HGP2 0.330 ! 2.536 37 | 38 | BOND C CA 39 | BOND CA N 40 | BOND CA CB 41 | BOND CB HB1 42 | BOND CB HB2 43 | BOND CB CG 44 | BOND CG HG1 45 | BOND CG HG2 46 | BOND CG CD 47 | BOND CD OE1 48 | BOND CD OE2 49 | BOND C O 50 | BOND C OXT 51 | BOND CA HA 52 | BOND N H1 53 | BOND N H2 54 | BOND H3 N 55 | IMPR C OXT O CA 56 | IMPR CD OE2 OE1 CG 57 | 58 | END 59 | 60 | read param card flex append 61 | * Parameters generated by analogy by 62 | * CHARMM General Force Field (CGenFF) program version 1.0.0 63 | * 64 | 65 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 66 | ! and 50 mean some basic validation is recommended; penalties higher than 67 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 68 | 69 | BONDS 70 | 71 | ANGLES 72 | 73 | DIHEDRALS 74 | 75 | IMPROPERS 76 | 77 | END 78 | RETURN 79 | -------------------------------------------------------------------------------- /InputFiles/Parameters/glutamine.str: -------------------------------------------------------------------------------- 1 | * Toppar stream file generated by 2 | * CHARMM General Force Field (CGenFF) program version 1.0.0 3 | * For use with CGenFF version 3.0.1 4 | * 5 | 6 | read rtf card append 7 | * Topologies generated by 8 | * CHARMM General Force Field (CGenFF) program version 1.0.0 9 | * 10 | 36 1 11 | 12 | ! "penalty" is the highest penalty score of the associated parameters. 13 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 14 | ! and 50 mean some basic validation is recommended; penalties higher than 15 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 16 | 17 | RESI GLNX 0.000 ! param penalty= 0.000 ; charge penalty= 102.994 18 | GROUP ! CHARGE CH_PENALTY 19 | ATOM C CG2O3 0.445 ! 99.918 20 | ATOM CA CG314 0.338 ! 102.994 21 | ATOM CB CG321 -0.190 ! 31.533 22 | ATOM HB1 HGA2 0.090 ! 2.500 23 | ATOM HB2 HGA2 0.090 ! 2.500 24 | ATOM CG CG321 -0.148 ! 8.543 25 | ATOM HG1 HGA2 0.090 ! 0.000 26 | ATOM HG2 HGA2 0.090 ! 0.000 27 | ATOM CD CG2O1 0.544 ! 8.169 28 | ATOM OE1 OG2D1 -0.544 ! 0.000 29 | ATOM NE2 NG2S2 -0.623 ! 0.000 30 | ATOM HE21 HGP1 0.310 ! 0.000 31 | ATOM HE22 HGP1 0.310 ! 0.000 32 | ATOM N NG3P3 -0.362 ! 37.436 33 | ATOM O OG2D2 -0.760 ! 8.256 34 | ATOM OXT OG2D2 -0.760 ! 8.256 35 | ATOM HA HGA1 0.090 ! 3.979 36 | ATOM H1 HGP2 0.330 ! 2.536 37 | ATOM H2 HGP2 0.330 ! 2.536 38 | ATOM H3 HGP2 0.330 ! 2.536 39 | 40 | BOND C CA 41 | BOND CA CB 42 | BOND CB HB1 43 | BOND CB HB2 44 | BOND CB CG 45 | BOND CG HG1 46 | BOND CG HG2 47 | BOND CG CD 48 | BOND CD OE1 49 | BOND CD NE2 50 | BOND NE2 HE21 51 | BOND NE2 HE22 52 | BOND CA N 53 | BOND C O 54 | BOND C OXT 55 | BOND CA HA 56 | BOND N H1 57 | BOND N H2 58 | BOND H3 N 59 | IMPR C OXT O CA 60 | IMPR CD CG NE2 OE1 61 | 62 | END 63 | 64 | read param card flex append 65 | * Parameters generated by analogy by 66 | * CHARMM General Force Field (CGenFF) program version 1.0.0 67 | * 68 | 69 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 70 | ! and 50 mean some basic validation is recommended; penalties higher than 71 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 72 | 73 | BONDS 74 | 75 | ANGLES 76 | 77 | DIHEDRALS 78 | 79 | IMPROPERS 80 | 81 | END 82 | RETURN 83 | -------------------------------------------------------------------------------- /InputFiles/Parameters/glycerate.str: -------------------------------------------------------------------------------- 1 | * Toppar stream file generated by 2 | * CHARMM General Force Field (CGenFF) program version 1.0.0 3 | * For use with CGenFF version 3.0.1 4 | * 5 | 6 | read rtf card append 7 | * Topologies generated by 8 | * CHARMM General Force Field (CGenFF) program version 1.0.0 9 | * 10 | 36 1 11 | 12 | ! "penalty" is the highest penalty score of the associated parameters. 13 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 14 | ! and 50 mean some basic validation is recommended; penalties higher than 15 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 16 | 17 | RESI GLA -1.000 ! param penalty= 5.500 ; charge penalty= 4.529 18 | GROUP ! CHARGE CH_PENALTY 19 | ATOM C1 CG2O3 0.626 ! 4.203 20 | ATOM O1 OG2D2 -0.760 ! 0.250 21 | ATOM O2 OG2D2 -0.760 ! 0.250 22 | ATOM C2 CG311 0.041 ! 4.529 23 | ATOM H1 HGA1 0.090 ! 0.000 24 | ATOM O3 OG311 -0.617 ! 3.624 25 | ATOM H2 HGP1 0.369 ! 3.268 26 | ATOM C3 CG321 0.060 ! 2.372 27 | ATOM H3 HGA2 0.090 ! 0.000 28 | ATOM H4 HGA2 0.090 ! 0.000 29 | ATOM O4 OG311 -0.649 ! 0.375 30 | ATOM H5 HGP1 0.420 ! 0.000 31 | 32 | BOND C1 O1 33 | BOND C1 O2 34 | BOND C1 C2 35 | BOND C2 H1 36 | BOND C2 O3 37 | BOND C2 C3 38 | BOND O3 H2 39 | BOND C3 H3 40 | BOND C3 H4 41 | BOND C3 O4 42 | BOND O4 H5 43 | IMPR C1 O1 O2 C2 44 | 45 | END 46 | 47 | read param card flex append 48 | * Parameters generated by analogy by 49 | * CHARMM General Force Field (CGenFF) program version 1.0.0 50 | * 51 | 52 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 53 | ! and 50 mean some basic validation is recommended; penalties higher than 54 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 55 | 56 | BONDS 57 | 58 | ANGLES 59 | CG2O3 CG311 OG311 45.00 109.00 ! ***** , from CG2O3 CG311 OG301, penalty= 5 60 | 61 | DIHEDRALS 62 | OG2D2 CG2O3 CG311 OG311 0.5500 2 180.00 ! ***** , from OG2D2 CG2O3 CG311 OG301, penalty= 5 63 | CG2O3 CG311 OG311 HGP1 0.3500 1 0.00 ! ***** , from CG2O5 CG311 OG311 HGP1, penalty= 5.5 64 | CG2O3 CG311 OG311 HGP1 0.3700 2 0.00 ! ***** , from CG2O5 CG311 OG311 HGP1, penalty= 5.5 65 | CG2O3 CG311 OG311 HGP1 0.0100 3 180.00 ! ***** , from CG2O5 CG311 OG311 HGP1, penalty= 5.5 66 | 67 | IMPROPERS 68 | 69 | END 70 | RETURN 71 | -------------------------------------------------------------------------------- /InputFiles/Parameters/malate.str: -------------------------------------------------------------------------------- 1 | * Toppar stream file generated by 2 | * CHARMM General Force Field (CGenFF) program version 1.0.0 3 | * For use with CGenFF version 3.0.1 4 | * 5 | 6 | read rtf card append 7 | * Topologies generated by 8 | * CHARMM General Force Field (CGenFF) program version 1.0.0 9 | * 10 | 36 1 11 | 12 | ! "penalty" is the highest penalty score of the associated parameters. 13 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 14 | ! and 50 mean some basic validation is recommended; penalties higher than 15 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 16 | 17 | RESI MAL -2.000 ! param penalty= 5.500 ; charge penalty= 6.482 18 | GROUP ! CHARGE CH_PENALTY 19 | ATOM O1 OG2D2 -0.760 ! 0.250 20 | ATOM C1 CG2O3 0.626 ! 4.203 21 | ATOM O2 OG2D2 -0.760 ! 0.250 22 | ATOM C2 CG311 0.041 ! 6.482 23 | ATOM H1 HGA1 0.090 ! 0.000 24 | ATOM O3 OG311 -0.615 ! 6.278 25 | ATOM C3 CG321 -0.272 ! 4.884 26 | ATOM H2 HGA2 0.090 ! 0.000 27 | ATOM H3 HGA2 0.090 ! 0.000 28 | ATOM C4 CG2O3 0.621 ! 2.466 29 | ATOM O4 OG2D2 -0.760 ! 0.000 30 | ATOM O5 OG2D2 -0.760 ! 0.000 31 | ATOM H4 HGP1 0.369 ! 3.268 32 | 33 | BOND O1 C1 34 | BOND C1 O2 35 | BOND C1 C2 36 | BOND C2 H1 37 | BOND C2 O3 38 | BOND C2 C3 39 | BOND C3 H2 40 | BOND C3 H3 41 | BOND C3 C4 42 | BOND C4 O4 43 | BOND C4 O5 44 | BOND O3 H4 45 | IMPR C1 O1 O2 C2 46 | IMPR C4 O5 O4 C3 47 | 48 | END 49 | 50 | read param card flex append 51 | * Parameters generated by analogy by 52 | * CHARMM General Force Field (CGenFF) program version 1.0.0 53 | * 54 | 55 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 56 | ! and 50 mean some basic validation is recommended; penalties higher than 57 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 58 | 59 | BONDS 60 | 61 | ANGLES 62 | CG2O3 CG311 OG311 45.00 109.00 ! ***** , from CG2O3 CG311 OG301, penalty= 5 63 | 64 | DIHEDRALS 65 | OG2D2 CG2O3 CG311 OG311 0.5500 2 180.00 ! ***** , from OG2D2 CG2O3 CG311 OG301, penalty= 5 66 | OG311 CG311 CG321 CG2O3 0.2000 3 0.00 ! ***** , from CG2O3 CG311 CG311 OG311, penalty= 4 67 | CG2O3 CG311 OG311 HGP1 0.3500 1 0.00 ! ***** , from CG2O5 CG311 OG311 HGP1, penalty= 5.5 68 | CG2O3 CG311 OG311 HGP1 0.3700 2 0.00 ! ***** , from CG2O5 CG311 OG311 HGP1, penalty= 5.5 69 | CG2O3 CG311 OG311 HGP1 0.0100 3 180.00 ! ***** , from CG2O5 CG311 OG311 HGP1, penalty= 5.5 70 | 71 | IMPROPERS 72 | 73 | END 74 | RETURN 75 | -------------------------------------------------------------------------------- /InputFiles/Parameters/metals/CHARMM_METAL.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/InputFiles/Parameters/metals/CHARMM_METAL.tgz -------------------------------------------------------------------------------- /InputFiles/Parameters/non_charmm/00readme: -------------------------------------------------------------------------------- 1 | 2 | This directory contains topology and parameter files that are 3 | compatible with CHARMM but are not part of the CHARMM force field 4 | development efforts. The parameters have been approved by the 5 | original developers, or individuals closely associated with those 6 | developers. However, they have not been exhaustively tested in the 7 | context of CHARMM and are not supported. Please carefully read the 8 | header sections of the respective files to obtain information on their 9 | proper use along with the appropriate references. 10 | 11 | BMS nucleic acid force field 12 | 13 | par_bms_dec03.prm 14 | top_bms_dec03.rtf 15 | 16 | AMBER Cornell 94 force field for proteins and nucleic acids and the 17 | 1998 variant of the nucleic acid parameters. Requires CHARMM compiled 18 | with AMBER keyword in pref.dat. Note that such versions of CHARMM can 19 | NOT be used with the CHARMM force field. 20 | 21 | top_amber_cornell.inp 22 | par_amber_cornell.inp 23 | par_amber_98.inp 24 | 25 | parm14sb_all.rtf, parm14sb_all.prm: added July 2015 26 | 27 | Additional versions of CHARMM compatible AMBER files may be obtained 28 | from Jeff Klauda's website: 29 | 30 | http://www.glue.umd.edu/~jbklauda/research/download.html 31 | or 32 | http://terpconnect.umd.edu/~jbklauda/research/download.html 33 | 34 | OPLS AA protein force field along with ligand parameters. Requires 35 | CHARMM compiled with OPLS keyword in pref.dat. 36 | 37 | top_opls_aa.inp 38 | par_opls_aa.inp 39 | par_opls_ligand.inp 40 | 41 | top_opls_aam.inp 42 | par_opls_aam.inp: added July 2015 43 | 44 | Version of Amber FF99SB* from Robert Best (not 45 | tested). e_corr_ff99sb.pdf contains the energy correction that 46 | converts the FFSB99 backbone potential to FFSB99* 47 | 48 | charmm_ff99sbstar.tgz 49 | 50 | Stream files containing various water models. Note that the water 51 | atom types are the same as in the TIP3P model such that the following 52 | files can NOT be used simultaneously with the TIP3P model in the 53 | default toppar_water_ions.str file. This can be overcome by changing 54 | the water atom types in the following files. 55 | 56 | Caution: The models with LPs fail with late versions of C36 57 | (post-fortran 90 conversion) and early versions of C37 58 | 59 | toppar_water_ions_spc.str 60 | toppar_water_ions_spc_e.str 61 | toppar_water_ions_tip3p_pme_b.str 62 | toppar_water_ions_tip3p_pme_f.str 63 | toppar_water_ions_tip4p.str 64 | toppar_water_ions_tip4p_2005.str 65 | toppar_water_ions_tip4p_ew.str 66 | toppar_water_ions_tip5p.str 67 | toppar_water_ions_tip5p_ew.str 68 | 69 | GROMACS 70 | 71 | A full representation of the charmm36 FFs is in the gromacs 72 | subdirectory. See mackerell lab web page for additional information. 73 | -------------------------------------------------------------------------------- /InputFiles/Parameters/non_charmm/gromacs/charmm36-mar2019.ff.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/InputFiles/Parameters/non_charmm/gromacs/charmm36-mar2019.ff.tgz -------------------------------------------------------------------------------- /InputFiles/Parameters/non_charmm/toppar_chloroform_dh.str: -------------------------------------------------------------------------------- 1 | * chloroform topper file in CHARMM format 2 | * 3 | 4 | ! Chloroform based on the original DH model from Dietz and Heinzinger (DH model) 5 | ! (W. Dietz, K. Heinzinger, Ber. Bunsen-Ges. Phys. Chem 1985, 89, 968) 6 | ! Translated into CHARMM format for the following work 7 | ! (Yu, W., He, X., Vanommeslaeghe, K. and MacKerell, A. D., J. Comput. Chem., 2012, 33, 2451–2468) 8 | ! Tested in CHARMM and shown to be compatible with CHARMM protein and CGenFF force fields. 9 | ! Just use "stream toppar_chloroform_dh.str" in your CHARMM input file 10 | 11 | 12 | read rtf card append 13 | * chloroform 14 | * 15 | 16 | MASS -1 HCM 1.00800 ! 17 | MASS -1 CLCM 35.45000 ! 18 | MASS -1 CCM 12.01100 ! 19 | 20 | RESI CCL3 0.000 21 | GROUP 22 | ATOM C CCM 0.179 23 | ATOM CL1 CLCM -0.087 24 | ATOM CL2 CLCM -0.087 25 | ATOM CL3 CLCM -0.087 26 | ATOM HX HCM 0.082 27 | BOND C CL1 C CL2 C CL3 C HX 28 | BOND CL1 CL2 CL1 CL3 !for shake 29 | BOND CL1 HX CL2 HX CL3 HX ! for shake 30 | ANGLE HX C CL1 HX C CL2 HX C CL3 31 | ANGLE CL1 C CL2 CL1 C CL3 CL2 C CL3 32 | PATCHING FIRS NONE LAST NONE 33 | 34 | END 35 | 36 | read param card flex append 37 | * chloroform 38 | * 39 | 40 | ATOMS 41 | MASS -1 HCM 1.00800 ! 42 | MASS -1 CLCM 35.45000 ! 43 | MASS -1 CCM 12.01100 ! 44 | 45 | BONDS 46 | CCM CLCM 500.0 1.758 47 | CCM HCM 500.0 1.100 48 | CLCM CLCM 0.0 2.9028314 49 | HCM CLCM 0.0 2.3383924 50 | 51 | ANGLES 52 | CLCM CCM CLCM 0.0 111.30 53 | HCM CCM CLCM 0.0 107.57 54 | 55 | 56 | DIHEDRALS 57 | 58 | IMPROPERS 59 | 60 | NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - 61 | cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 62 | 63 | CCM 0.0 -0.102 1.9082 ! 64 | CLCM 0.0 -0.300 1.9306 ! 65 | HCM 0.0 -0.020 1.2347 ! 66 | 67 | END 68 | 69 | RETURN 70 | 71 | -------------------------------------------------------------------------------- /InputFiles/Parameters/silicates/00README: -------------------------------------------------------------------------------- 1 | 2 | CHARMM force field parameters have been recently developed for 3 | silicates and aluminumsilicates. This document shows how to set up 4 | input files for a slab of (011) quartz surface, taking advantage of 5 | the ability of CHARMM to perform MD simulations of peridic systems. 6 | 7 | Pedro Lopes and Alexander D. MacKerell, Jr. 8 | 9 | An auxiliary program, patchfind, has been developed to help in the 10 | definition of the patches between atoms in the primitive cell and 11 | neighbouring cells. Lists of bonds, angles and dihedrals, with the 12 | assignment of atoms along particular directions, are produced. You 13 | can find patchfind.x in ./code directory. 14 | 15 | The topology and parameter file is in the ./toppar subdirectory 16 | 17 | Steps for successful use of silicates and aluminumsilicates parameters 18 | in modeling surfaces: 19 | 20 | 1) Primitive unit cell of the surface in XYZ format (input.xyz): the 21 | surface has to be oriented along the X-Y plane. X is made to 22 | correspond to the crystalline a-vector and Y to the crystalline 23 | b-vector. c is orthogonal to a and b. 24 | 25 | 2) crystal.dat file: contains the a, b, c, alpha, beta and gamma 26 | crystal parameters: 27 | 28 | 7.3000 29 | 4.9100 30 | 44.5000 31 | 90.0 32 | 90.0 33 | 109.6517 34 | 35 | 3) run the program patchfind.x: if no mistakes were made it produces a 36 | list of bonds, angles and torsions that can be used to define the 37 | patches between the primitive and neigbouring cells. Common mistakes 38 | are made in the definition of the crystal parameters. The space is 39 | divided according to the following drawing. The priminitve cell is 40 | always 1. Replica along the a-vector is refered as XX or 2 and replica 41 | along the b-vector is refered as YY or 3. XY or 4 is the cell 42 | resulting from a+b. 43 | 44 | To run patchfind.x ./code/patchfind.x > patches.dat 45 | 46 | ----------------------- 47 | | | | 48 | | 3 | 4 | 49 | | YY | XY | 50 | | | | 51 | ----------------------- 52 | | | | 53 | | 1 | 2 | 54 | |Primitive | XX | 55 | | | | 56 | ----------------------- 57 | 58 | Example output is: 59 | 60 | Torsions along XX and YY 61 | 17 1 9 25 3 1 1 2 62 | 18 22 30 27 2 1 1 3 63 | 64 | In this case both torsions span tree cells: primitive, XX and YY. 65 | 66 | With this information the creation of the topology file is 67 | straightforward. 68 | 69 | 4) Create topology file: an example for quartz (011), 70 | is available in ./toppar/top_silicates.inp 71 | 72 | 5) A CHARMM input file, test.inp, is included. It reads the primitive 73 | cell, replicates 8x5 times the primitive cell to create the unit cell, 74 | then generates the images and patches the images. Required files are 75 | top_silicates.inp, par_silicates.inp, params.str, crystal.img and 76 | image_patch.str. 77 | 78 | 79 | -------------------------------------------------------------------------------- /InputFiles/Parameters/silicates/code/cell.f: -------------------------------------------------------------------------------- 1 | subroutine cell(alen,blen,clen,alpha,beta,gamma) 2 | implicit none 3 | c 4 | double precision alpha,beta,gamma 5 | double precision alen,blen,clen 6 | integer iout 7 | c 8 | c initialize periodic lengths and angles 9 | c 10 | iout = 6 11 | 12 | alen = 0.0d0 13 | blen = 0.0d0 14 | clen = 0.0d0 15 | alpha = 0.0d0 16 | beta = 0.0d0 17 | gamma = 0.0d0 18 | 19 | open (11,file='crystal.dat',status='old') 20 | read(11,*) alen,blen,clen,alpha,beta,gamma 21 | close (11) 22 | c 23 | c checck unspecified periodic lengths and angles 24 | c 25 | if (alen .eq. 0.0d0) write(iout,'(/,a)') 'a lenght not set' 26 | if (blen .eq. 0.0d0) write(iout,'(/,a)') 'b lenght not set' 27 | if (clen .eq. 0.0d0) write(iout,'(/,a)') 'c lenght not set' 28 | if (alpha .eq. 0.0d0) write(iout,'(/,a)') 'alpha not set' 29 | if (beta .eq. 0.0d0) write(iout,'(/,a)') 'beta not set' 30 | if (gamma .eq. 0.0d0) write(iout,'(/,a)') 'gamma not set' 31 | c 32 | c stop if lengths or angles are nought 33 | c 34 | if (alen.eq.0.0d0 .or. blen.eq.0.0d0 35 | & .or. clen.eq.90.0d0) stop 36 | if (alpha.eq.0.0d0 .or. beta.eq.0.0d0 37 | & .or. gamma.eq.90.0d0) stop 38 | 39 | return 40 | end 41 | -------------------------------------------------------------------------------- /InputFiles/Parameters/silicates/code/compile.txt: -------------------------------------------------------------------------------- 1 | 2 | g77 -o patchfind.x patchfind.f crystal.f cell.f 3 | 4 | -------------------------------------------------------------------------------- /InputFiles/Parameters/silicates/code/crystal.dat: -------------------------------------------------------------------------------- 1 | 7.3000 2 | 4.9100 3 | 44.5000 4 | 90.0 5 | 90.0 6 | 109.6517 7 | 8 | -------------------------------------------------------------------------------- /InputFiles/Parameters/silicates/code/input.xyz: -------------------------------------------------------------------------------- 1 | 40 2 | 3 | Si 4.118 4.481 -12.830 4 | Si 0.121 3.053 -9.489 5 | Si 3.423 1.626 -6.147 6 | Si 6.726 0.198 -2.806 7 | O 3.980 2.880 -12.662 8 | O -0.018 1.453 -9.320 9 | O 3.285 0.025 -5.979 10 | O 4.936 3.222 -2.638 11 | O 5.654 4.910 -12.703 12 | O 1.656 3.483 -9.362 13 | O 4.959 2.055 -6.020 14 | O 0.961 0.628 -2.679 15 | O -0.396 3.385 -10.982 16 | O 2.906 1.958 -7.641 17 | O 6.209 0.530 -4.300 18 | O 2.211 -0.897 -0.959 19 | O 4.828 0.576 -11.756 20 | O -0.821 3.772 -8.414 21 | O 2.481 2.345 -5.073 22 | O 5.784 0.917 -1.732 23 | Si 3.707 1.727 -11.588 24 | Si 5.358 4.923 -8.246 25 | Si 1.360 3.496 -4.905 26 | Si 4.663 2.068 -1.564 27 | Si -0.198 4.393 -12.209 28 | Si 3.105 2.966 -8.867 29 | Si 6.407 1.538 -5.526 30 | Si 2.410 0.110 -2.185 31 | O 3.896 2.311 -10.094 32 | O 5.547 5.508 -6.753 33 | O 1.550 4.080 -3.411 34 | O 4.852 2.653 -0.070 35 | O 2.246 1.087 -11.715 36 | O 3.898 4.283 -8.373 37 | O -0.100 2.856 -5.032 38 | O 3.203 1.428 -1.691 39 | H 3.601 4.813 -14.324 40 | H 2.728 -1.229 0.535 41 | H 0.594 3.739 -13.435 42 | H 4.061 3.307 1.156 43 | -------------------------------------------------------------------------------- /InputFiles/Parameters/silicates/code/patchfind.x: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/InputFiles/Parameters/silicates/code/patchfind.x -------------------------------------------------------------------------------- /InputFiles/Parameters/silicates/crystal.dat: -------------------------------------------------------------------------------- 1 | 7.3000 2 | 4.9100 3 | 44.5000 4 | 90.0 5 | 90.0 6 | 109.6517 7 | 8 | -------------------------------------------------------------------------------- /InputFiles/Parameters/silicates/crystal.img: -------------------------------------------------------------------------------- 1 | ! Description of periodic boundary conditions 2 | ! 3 | ! Images 4 | ! 5 | ! z = 0 6 | ! 7 | ! 8 3 5 8 | ! 2 prim 1 9 | ! 6 4 7 10 | ! 11 | ! z = +(w1,w2,w3) 12 | ! 13 | ! 21 15 19 14 | ! 13 9 11 15 | ! 23 17 25 16 | ! 17 | ! z = -(w1,w2,w3) 18 | ! 19 | ! 26 18 24 20 | ! 12 10 14 21 | ! 20 16 22 22 | ! 23 | * Image generation 24 | * 25 | scale 1 1 1 26 | 27 | IMAGE qi1 28 | TRANslate @bigu1 @bigu2 @bigu3 29 | 30 | IMAGE qi2 31 | DEFIne INVErse qi1 32 | 33 | IMAGE qi3 34 | TRANslate @bigv1 @bigv2 @bigv3 35 | 36 | IMAGE qi4 37 | DEFIne INVErse qi3 38 | 39 | IMAGE qi5 40 | DEFIne qi1 qi3 41 | 42 | IMAGE qi6 43 | DEFIne INVErse qi5 44 | 45 | IMAGE qi7 46 | DEFIne qi1 qi4 47 | 48 | IMAGE qi8 49 | DEFIne INVErse qi7 50 | 51 | IMAGE qi9 52 | TRANslate @bigw1 @bigw2 @bigw3 53 | 54 | IMAGE qi10 55 | DEFIne INVErse qi9 56 | 57 | IMAGE qi11 58 | DEFIne qi1 qi9 59 | 60 | IMAGE qi12 61 | DEFIne INVErse qi11 62 | 63 | IMAGE qi13 64 | DEFIne qi2 qi9 65 | 66 | IMAGE qi14 67 | DEFIne INVErse qi13 68 | 69 | IMAGE qi15 70 | DEFIne qi3 qi9 71 | 72 | IMAGE qi16 73 | DEFIne INVErse qi15 74 | 75 | IMAGE qi17 76 | DEFIne qi4 qi9 77 | 78 | IMAGE qi18 79 | DEFIne INVErse qi17 80 | 81 | IMAGE qi19 82 | DEFIne qi5 qi9 83 | 84 | IMAGE qi20 85 | DEFIne INVErse qi19 86 | 87 | IMAGE qi21 88 | DEFIne qi8 qi9 89 | 90 | IMAGE qi22 91 | DEFIne INVErse qi21 92 | 93 | IMAGE qi23 94 | DEFIne qi6 qi9 95 | 96 | IMAGE qi24 97 | DEFIne INVErse qi23 98 | 99 | IMAGE qi25 100 | DEFIne qi7 qi9 101 | 102 | IMAGE qi26 103 | DEFIne INVErse qi25 104 | 105 | end 106 | 107 | -------------------------------------------------------------------------------- /InputFiles/Parameters/silicates/image_patch.str: -------------------------------------------------------------------------------- 1 | 2 | update inbf 0 ihbf 0 imgfrq 011 cutim @3 3 | 4 | ! Now apply patches around the perimeter 5 | ! 6 | 7 | !In x direction 8 | ! 9 | ! py | iy 10 | ! prim px | ix image 11 | ! 12 | 13 | set counn 1 14 | label loop2 15 | calc px = @counn * @n 16 | calc ix = @px - @n + 1 17 | calc py = @px + @n 18 | calc iy = @py - @n + 1 19 | impa 011A prim q@px 1 qi1 q@ix 1 setup warn 20 | 21 | impa 011C prim q@px 1 qi1 q@iy 1 setup warn 22 | 23 | impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn 24 | 25 | impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn 26 | 27 | impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn 28 | 29 | impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn 30 | 31 | 32 | 33 | calc counn = @counn + 1 34 | if counn lt @m goto loop2 35 | ! corner cells will be treated later 36 | 37 | ! In y direction 38 | ! 39 | ! image 40 | ! iy ix 41 | ! --------------- 42 | ! py px 43 | ! prim 44 | 45 | set counm 1 46 | label loop3 47 | calc py = (@m - 1) * @n + @counm 48 | calc iy = @counm 49 | calc px = @py + 1 50 | calc ix = @iy + 1 51 | impa 011B prim q@py 1 qi3 q@iy 1 setup warn 52 | impa 011C prim q@py 1 qi3 q@ix 1 setup warn 53 | 54 | impa 011D prim q@py 1 qi3 q@ix 1 qi3 q@iy 1 setup warn 55 | 56 | impa 011E qi3 q@iy 1 prim q@py 1 prim q@px 1 setup warn 57 | 58 | impa 011F prim q@py 1 prim q@px 1 qi3 q@ix 1 setup warn 59 | 60 | impa 011G prim q@py 1 qi3 q@iy 1 qi3 q@ix 1 setup warn 61 | 62 | 63 | 64 | calc counm = @counm +1 65 | if counm lt @n goto loop3 66 | 67 | ! Now corner cells 68 | calc py = (@m - 1) * @n + 1 69 | calc iy = 1 70 | calc ix = @n 71 | 72 | calc py = @m*@n 73 | calc ix = (@m - 1) * @n + 1 74 | calc iy = @n 75 | set ixy 1 76 | impa 011A prim q@py 1 qi1 q@ix 1 setup warn 77 | 78 | impa 011B prim q@py 1 qi3 q@iy 1 setup warn 79 | 80 | impa 011C prim q@py 1 qi5 q@ixy 1 setup warn 81 | 82 | impa 011D prim q@py 1 qi5 q@ixy 1 qi3 q@iy 1 setup warn 83 | 84 | impa 011E qi3 q@iy 1 prim q@py 1 qi1 q@ix 1 setup warn 85 | 86 | impa 011F prim q@py 1 qi1 q@ix 1 qi5 q@ixy 1 setup warn 87 | 88 | impa 011G prim q@py 1 qi3 q@iy 1 qi5 q@ixy 1 setup warn 89 | 90 | 91 | 92 | ! Below info for testing only 93 | ! PRINT IMAG PSF 94 | 95 | -------------------------------------------------------------------------------- /InputFiles/Parameters/silicates/input.xyz: -------------------------------------------------------------------------------- 1 | 40 2 | 3 | Si 4.118 4.481 -12.830 4 | Si 0.121 3.053 -9.489 5 | Si 3.423 1.626 -6.147 6 | Si 6.726 0.198 -2.806 7 | O 3.980 2.880 -12.662 8 | O -0.018 1.453 -9.320 9 | O 3.285 0.025 -5.979 10 | O 4.936 3.222 -2.638 11 | O 5.654 4.910 -12.703 12 | O 1.656 3.483 -9.362 13 | O 4.959 2.055 -6.020 14 | O 0.961 0.628 -2.679 15 | O -0.396 3.385 -10.982 16 | O 2.906 1.958 -7.641 17 | O 6.209 0.530 -4.300 18 | O 2.211 -0.897 -0.959 19 | O 4.828 0.576 -11.756 20 | O -0.821 3.772 -8.414 21 | O 2.481 2.345 -5.073 22 | O 5.784 0.917 -1.732 23 | Si 3.707 1.727 -11.588 24 | Si 5.358 4.923 -8.246 25 | Si 1.360 3.496 -4.905 26 | Si 4.663 2.068 -1.564 27 | Si -0.198 4.393 -12.209 28 | Si 3.105 2.966 -8.867 29 | Si 6.407 1.538 -5.526 30 | Si 2.410 0.110 -2.185 31 | O 3.896 2.311 -10.094 32 | O 5.547 5.508 -6.753 33 | O 1.550 4.080 -3.411 34 | O 4.852 2.653 -0.070 35 | O 2.246 1.087 -11.715 36 | O 3.898 4.283 -8.373 37 | O -0.100 2.856 -5.032 38 | O 3.203 1.428 -1.691 39 | H 3.601 4.813 -14.324 40 | H 2.728 -1.229 0.535 41 | H 0.594 3.739 -13.435 42 | H 4.061 3.307 1.156 43 | -------------------------------------------------------------------------------- /InputFiles/Parameters/silicates/params.str: -------------------------------------------------------------------------------- 1 | * Parameters for simulation of on crystal surfaces 2 | * 3 | 4 | ! Generation of n cells along U and m cells along V 5 | ! Used to specify the surface size from the primitive cell 6 | ! k is the number of replicas along Z 7 | 8 | set n 5 9 | set m 8 10 | set k 1 11 | 12 | calc nm = @n * @m * @k 13 | 14 | ! 15 | ! U |__2| V 16 | !|__1|__2| 1-->2 |__1| 1-->2 17 | ! 18 | ! 19 | ! Q(M-1)*N+1 Q(M-1)*N+2 ..... QM*N 20 | ! ---------------------------------------- 21 | ! . . . . . 22 | ! . . . . . 23 | ! . . . . . 24 | ! ----------------------------------------- 25 | ! QN+1 QN+2 26 | ! ----------------------------------------- 27 | ! Q1 Q2 Q3 Q4 Q5 .... QN 28 | ! ----------------------------------------- 29 | ! 30 | ! 31 | ! Based on the PBC for the surface one has to set the values of U (a-vector), 32 | ! V (b-vector) and Z (c-vector). The angle between U and V is theta. 33 | 34 | !PBC 7.3000 4.9100 109.6517 (P1) 35 | 36 | set U = 7.3000 37 | set V = 4.9100 38 | set Z = 50.000 39 | 40 | set theta = 109.6517 41 | 42 | set radian = 57.29577951308232088 43 | calc theta = @theta - 90.0 44 | calc theta = @theta/@radian 45 | 46 | 47 | !unit cell translation parameters 48 | set u1 @U 49 | set u2 0.0 50 | set u3 0.0 51 | 52 | calc v1 @V*sin(@theta) 53 | calc v1 = -1*@v1 54 | calc v2 @V*cos(@theta) 55 | set v3 0.0 56 | 57 | set w1 0.0 58 | set w2 0.0 59 | set w3 @Z 60 | 61 | !Define translational vectors for images 62 | 63 | calc bigu1 = @n * @u1 64 | calc bigu2 = @n * @u2 65 | calc bigu3 = @n * @u3 66 | 67 | calc bigv1 = @m * @v1 68 | calc bigv2 = @m * @v2 69 | calc bigv3 = @m * @v3 70 | 71 | calc bigw1 = @k * @w1 72 | calc bigw2 = @k * @w2 73 | calc bigw3 = @k * @w3 74 | 75 | 76 | -------------------------------------------------------------------------------- /InputFiles/Parameters/silicates/supp_mat_oct05.tar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/InputFiles/Parameters/silicates/supp_mat_oct05.tar -------------------------------------------------------------------------------- /InputFiles/Parameters/stream/lipid/toppar_all36_lipid_cationpi_wyf.str: -------------------------------------------------------------------------------- 1 | * NBFIX parameters for cation-pi interactions (CHARMM36-WYF) 2 | * between phenol-TMA, benzene-TMA and indole-TMA 3 | * also for (tyrosine,phenylalanine,tryptophan)-PC lipids/choline 4 | * 5 | 6 | !reference Khan, MacKerell, Jr., and Reuter, "Cation-π Interactions 7 | !between Methylated Ammonium Groups and Tryptophan in the CHARMM36 8 | !Additive Force Field," J. Chem. Theory Comput. 2019, 15, 1, 7-12, 9 | !DOI: 10.1021/acs.jctc.8b00839 10 | 11 | read para card flex append 12 | * NBFIX parameters for cation-pi 13 | * 14 | 15 | NBFIX 16 | !!! NBFIX for cation-pi between phenol-TMA & benzene-TMA, CGenFF 17 | CG2R61 CG334 -0.2081 4.2074 18 | CG2R61 NG3P0 -0.2400 3.8424 19 | !!! NBFIX for cation-pi between tyrosine-PC lipids & phenylalanine-PC, C36 protein-lipids 20 | CA CTL5 -0.2081 4.2074 21 | CA NTL -0.2400 3.8424 22 | !!! NBFIX for cation-pi between tyrosine-choline & phenylalanine-choline, C36 protein-CGenFF 23 | CA CG334 -0.2081 4.2074 24 | CA NG3P0 -0.2400 3.8424 25 | 26 | !!! NBFIX for indole-tma / indole-choline, CGenFF 27 | CG2R51 CG334 -0.04205 4.3150 28 | CG2R51 NG3P0 -0.1000 3.9500 29 | NG2R51 CG334 -0.9241 4.0650 30 | NG2R51 NG3P0 -0.8000 3.7000 31 | CG2RC0 CG334 -0.01731 4.0750 32 | CG2RC0 NG3P0 -0.01071 3.7100 33 | !!! NBFIX for cation-pi between tryptophan-PC, C36-protein lipids 34 | CY CTL5 -0.04205 4.3150 35 | CY NTL -0.1000 3.9500 36 | NY CTL5 -0.9241 4.0650 37 | NY NTL -0.8000 3.7000 38 | CPT CTL5 -0.01731 4.0750 39 | CPT NTL -0.01071 3.7100 40 | CAI CTL5 -0.2081 4.2074 41 | CAI NTL -0.2400 3.8424 42 | !!! NBFIX for cation-pi between tryptophan-choline, C36 protein-CGenFF 43 | CY CG334 -0.04205 4.3150 44 | CY NG3P0 -0.1000 3.9500 45 | NY CG334 -0.9241 4.0650 46 | NY NG3P0 -0.8000 3.7000 47 | CPT CG334 -0.01731 4.0750 48 | CPT NG3P0 -0.01071 3.7100 49 | CAI CG334 -0.2081 4.2074 50 | CAI NG3P0 -0.2400 3.8424 51 | 52 | end 53 | 54 | -------------------------------------------------------------------------------- /InputFiles/Parameters/stream/lipid/toppar_all36_lipid_list.str: -------------------------------------------------------------------------------- 1 | * stream file to read all the rtf, para and lipid stream files 2 | * carbohydrate stream files added in 2016/2017 3 | * 4 | 5 | ! read water 6 | stream @water 7 | 8 | ! lipid 9 | ! read the topology 10 | open unit 9 read form name @a 11 | read rtf card append unit 9 12 | 13 | ! read the parameters 14 | open unit 9 read form name @b 15 | read para card append flex unit 9 16 | 17 | !protein 18 | ! append the topology 19 | open unit 9 read form name @c 20 | read rtf card append unit 9 21 | 22 | ! append the parameters 23 | open unit 9 read form name @d 24 | read para card flex append unit 9 25 | 26 | ! nucleic acid 27 | ! append the topology 28 | open unit 9 read form name @e 29 | read rtf card append unit 9 30 | 31 | ! append the parameters 32 | open unit 9 read form name @f 33 | read para card flex append unit 9 34 | 35 | ! carbohydrate 36 | ! append the topology 37 | open unit 9 read form name @g 38 | read rtf card append unit 9 39 | 40 | ! append the parameters 41 | open unit 9 read form name @h 42 | read para card flex append unit 9 43 | 44 | ! CGenFF 45 | ! append the topology 46 | open unit 9 read form name @i 47 | read rtf card append unit 9 48 | 49 | ! append the parameters 50 | open unit 9 read form name @j 51 | read para card flex append unit 9 52 | 53 | stream @toppar/stream/lipid/toppar_all36_lipid_bacterial.str 54 | stream @toppar/stream/lipid/toppar_all36_lipid_cationpi_wyf.str 55 | stream @toppar/stream/lipid/toppar_all36_lipid_miscellaneous.str 56 | stream @toppar/stream/lipid/toppar_all36_lipid_cholesterol.str 57 | stream @toppar/stream/lipid/toppar_all36_lipid_sphingo.str 58 | stream @toppar/stream/lipid/toppar_all36_lipid_detergent.str 59 | stream @toppar/stream/lipid/toppar_all36_lipid_ether.str 60 | stream @toppar/stream/lipid/toppar_all36_lipid_yeast.str 61 | stream @toppar/stream/lipid/toppar_all36_lipid_inositol.str 62 | stream @toppar/stream/lipid/toppar_all36_lipid_cardiolipin.str 63 | stream @toppar/stream/lipid/toppar_all36_lipid_prot.str 64 | stream @toppar/stream/lipid/toppar_all36_lipid_model.str 65 | stream @toppar/stream/lipid/toppar_all36_lipid_lps.str 66 | stream @toppar/stream/lipid/toppar_all36_lipid_cationpi_wyf.str 67 | 68 | stream @toppar/stream/carb/toppar_all36_carb_model.str 69 | stream @toppar/stream/carb/toppar_all36_carb_imlab.str 70 | stream @toppar/stream/carb/toppar_all36_carb_glycolipid.str 71 | stream @toppar/stream/carb/toppar_all36_carb_glycopeptide.str 72 | 73 | return 74 | 75 | -------------------------------------------------------------------------------- /InputFiles/Parameters/stream/misc/toppar_dum_noble_gases.str: -------------------------------------------------------------------------------- 1 | * Toplogy and parameter information for helium, neon and a dummy atom. 2 | * 3 | 4 | !Testcase 5 | !test_dum_nobel_gases.inp 6 | 7 | !test "append" to determine if previous toppar files have been read and 8 | !add append to "read rtf card" if true 9 | set nat ?NATC 10 | set app 11 | !We're exploiting what is arguably a bug in the parser. On the left hand side, 12 | !the quotes have proirity, so NAT is correctly substituted. On the right hand 13 | !side, the ? has priority and NATC" (sic) is not a valid substitution... 14 | if "@NAT" ne "?NATC" if @nat ne 0 set app append 15 | 16 | read rtf card @app 17 | * Topology for helium, neon and a dummy atom. 18 | * 19 | 31 1 20 | 21 | MASS -1 HE 4.00260 ! helium 22 | MASS -1 NE 20.17970 ! neon 23 | MASS -1 DUM 0.00000 ! dummy atom 24 | 25 | RESI HE1 0.00 ! helium 26 | GROUP 27 | ATOM HE01 HE 0.00 28 | PATCHING FIRST NONE LAST NONE 29 | 30 | RESI NE1 0.00 ! neon 31 | GROUP 32 | ATOM NE01 NE 0.00 33 | PATCHING FIRST NONE LAST NONE 34 | 35 | RESI DUM 0.00 ! DUMMY ATOM 36 | GROUP 37 | ATOM DUM DUM 0.00 38 | PATCHING FIRST NONE LAST NONE 39 | 40 | end 41 | 42 | read para card flex @app 43 | * Parameters for helium, neon and a dummy atom. 44 | * 45 | 46 | ATOMS 47 | MASS -1 HE 4.00260 ! helium 48 | MASS -1 NE 20.17970 ! neon 49 | MASS -1 DUM 0.00000 ! dummy atom 50 | 51 | NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - 52 | cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 53 | 54 | DUM 0.000000 -0.000000 0.000000 55 | HE 0.000000 -0.021270 1.480000 56 | NE 0.000000 -0.085450 1.530000 57 | 58 | end 59 | 60 | return 61 | 62 | 63 | -------------------------------------------------------------------------------- /InputFiles/Parameters/stream/misc/toppar_hbond.str: -------------------------------------------------------------------------------- 1 | * This stream file is for hydrogen bond analysis ONLY. 2 | * It WILL change your energy function (not for the better) 3 | * by adding an HBOND energy term. Use at your own risk. 4 | * NOTE: The charmm potential energy function is designed NOT 5 | * to include an explicit hydrogen bond term. Therefore, use 6 | * of the following hydrogen bond parameters will lead to incorrect 7 | * results. 8 | * 9 | 10 | !Parent files that have to be read prior to streaming this file 11 | !top_all36_na.rtf or the protein or lipid top file 12 | !par_all36_na.prm or the protein or lipid par file 13 | 14 | !Testcase 15 | !test_hbond.inp 16 | 17 | read para card flex append 18 | * hbond parameters for analysis only 19 | * 20 | 21 | EQUIVALENCE 22 | NALL 10 N* 23 | OALL 10 O* 24 | SALL 10 S* 25 | 26 | HBOND AEXP 4 REXP 6 HAEX 2 AAEX 2 NOACCEPTORS HBNOEXCLUSIONS ALL - 27 | CUTHB 6.0 CTOFHB 5.0 CTONHB 4.0 CUTHA 100.0 CTOFHA 90.0 CTONHA 90.0 28 | NALL NALL -5.000 3.0000 29 | NALL OALL -4.900 2.9000 30 | OALL NALL -4.850 2.8500 31 | OALL OALL -4.750 2.7500 32 | SALL NALL -3.500 3.0000 33 | SALL OALL -3.500 2.9000 34 | 35 | END 36 | 37 | return 38 | 39 | -------------------------------------------------------------------------------- /InputFiles/Parameters/valine.str: -------------------------------------------------------------------------------- 1 | * Toppar stream file generated by 2 | * CHARMM General Force Field (CGenFF) program version 1.0.0 3 | * For use with CGenFF version 3.0.1 4 | * 5 | 6 | read rtf card append 7 | * Topologies generated by 8 | * CHARMM General Force Field (CGenFF) program version 1.0.0 9 | * 10 | 36 1 11 | 12 | ! "penalty" is the highest penalty score of the associated parameters. 13 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 14 | ! and 50 mean some basic validation is recommended; penalties higher than 15 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 16 | 17 | RESI VALX 0.000 ! param penalty= 0.000 ; charge penalty= 103.055 18 | GROUP ! CHARGE CH_PENALTY 19 | ATOM HA HGA1 0.090 ! 4.020 20 | ATOM CA CG314 0.350 ! 103.055 21 | ATOM N NG3P3 -0.355 ! 37.562 22 | ATOM H1 HGP2 0.330 ! 2.540 23 | ATOM H2 HGP2 0.330 ! 2.540 24 | ATOM CB CG311 -0.086 ! 31.618 25 | ATOM HB HGA1 0.090 ! 2.542 26 | ATOM CG1 CG331 -0.272 ! 2.684 27 | ATOM HG11 HGA3 0.090 ! 0.330 28 | ATOM HG12 HGA3 0.090 ! 0.330 29 | ATOM HG13 HGA3 0.090 ! 0.330 30 | ATOM CG2 CG331 -0.272 ! 2.684 31 | ATOM HG21 HGA3 0.090 ! 0.330 32 | ATOM HG22 HGA3 0.090 ! 0.330 33 | ATOM HG23 HGA3 0.090 ! 0.330 34 | ATOM C CG2O3 0.445 ! 99.967 35 | ATOM O OG2D2 -0.760 ! 8.256 36 | ATOM OXT OG2D2 -0.760 ! 8.256 37 | ATOM H3 HGP2 0.330 ! 2.540 38 | 39 | BOND HA CA 40 | BOND CA N 41 | BOND CA CB 42 | BOND CA C 43 | BOND N H1 44 | BOND N H2 45 | BOND CB HB 46 | BOND CB CG1 47 | BOND CB CG2 48 | BOND CG1 HG11 49 | BOND CG1 HG12 50 | BOND CG1 HG13 51 | BOND CG2 HG21 52 | BOND CG2 HG22 53 | BOND CG2 HG23 54 | BOND C O 55 | BOND C OXT 56 | BOND H3 N 57 | IMPR C OXT O CA 58 | 59 | END 60 | 61 | read param card flex append 62 | * Parameters generated by analogy by 63 | * CHARMM General Force Field (CGenFF) program version 1.0.0 64 | * 65 | 66 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 67 | ! and 50 mean some basic validation is recommended; penalties higher than 68 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 69 | 70 | BONDS 71 | 72 | ANGLES 73 | 74 | DIHEDRALS 75 | 76 | IMPROPERS 77 | 78 | END 79 | RETURN 80 | -------------------------------------------------------------------------------- /InputFiles/colvars.in: -------------------------------------------------------------------------------- 1 | # colvar script to keep protein centered 2 | 3 | colvarsTrajFrequency 5000 4 | 5 | colvar { 6 | name dist 7 | 8 | distance { 9 | 10 | group1 { # protein CA atom selection 11 | psfSegID A 12 | atomNameResidueRange CA 10-60 13 | } 14 | group2 { dummyAtom ( 0.0, 0.0, 0.0) } 15 | } 16 | } 17 | 18 | harmonic { 19 | colvars dist 20 | centers 0 21 | forceConstant 0.2 22 | } 23 | 24 | 25 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Copyright (c) 2014, mkuiper 2 | All rights reserved. 3 | 4 | Redistribution and use in source and binary forms, with or without 5 | modification, are permitted provided that the following conditions are met: 6 | 7 | * Redistributions of source code must retain the above copyright notice, this 8 | list of conditions and the following disclaimer. 9 | 10 | * Redistributions in binary form must reproduce the above copyright notice, 11 | this list of conditions and the following disclaimer in the documentation 12 | and/or other materials provided with the distribution. 13 | 14 | * Neither the name of the {organization} nor the names of its 15 | contributors may be used to endorse or promote products derived from 16 | this software without specific prior written permission. 17 | 18 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 19 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 20 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 21 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 22 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 23 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 24 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 25 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 26 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 27 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 28 | 29 | -------------------------------------------------------------------------------- /Project/MovieBox/Examples/untitled.blend: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/Project/MovieBox/Examples/untitled.blend -------------------------------------------------------------------------------- /Project/MovieBox/Examples/viewpoints_01.tcl: -------------------------------------------------------------------------------- 1 | #This file contains viewpoints for a VMD script, view_change.tcl. 2 | #Type 'source viewpoints_01.tcl' from the VMD command window to load these viewpoints. 3 | 4 | set viewpoints(1,0,0) { {{0.894576 -0.25254 0.368721 0} {0.0737917 0.897178 0.435453 0} {-0.440777 -0.362336 0.821231 0} {0 0 0 1}} } 5 | 6 | set viewpoints(1,0,1) { {{1 0 0 -22.703} {0 1 0 13.4484} {0 0 1 -12.2882} {0 0 0 1}} } 7 | 8 | set viewpoints(1,0,2) { {{0.0107216 0 0 0} {0 0.0107216 0 0} {0 0 0.0107216 0} {0 0 0 1}} } 9 | 10 | set viewpoints(1,0,3) { {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}} } 11 | 12 | set viewpoints(2,0,0) { {{0.881652 -0.245906 0.402763 0} {0.0330624 0.883585 0.467095 0} {-0.470737 -0.398498 0.787146 0} {0 0 0 1}} } 13 | 14 | set viewpoints(2,0,1) { {{1 0 0 -22.703} {0 1 0 13.4484} {0 0 1 -12.2882} {0 0 0 1}} } 15 | 16 | set viewpoints(2,0,2) { {{0.0266681 0 0 0} {0 0.0266681 0 0} {0 0 0.0266681 0} {0 0 0 1}} } 17 | 18 | set viewpoints(2,0,3) { {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}} } 19 | 20 | set viewpoints(3,0,0) { {{0.914673 -0.282847 0.288748 0} {0.138957 0.890867 0.432485 0} {-0.379563 -0.355457 0.854156 0} {0 0 0 1}} } 21 | 22 | set viewpoints(3,0,1) { {{1 0 0 -22.703} {0 1 0 13.4484} {0 0 1 -12.2882} {0 0 0 1}} } 23 | 24 | set viewpoints(3,0,2) { {{0.0460641 0 0 0} {0 0.0460641 0 0} {0 0 0.0460641 0} {0 0 0 1}} } 25 | 26 | set viewpoints(3,0,3) { {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}} } 27 | 28 | set viewpoints(4,0,0) { {{0.826396 0.158739 0.540254 0} {-0.328763 0.91495 0.234049 0} {-0.457154 -0.371031 0.808299 0} {0 0 0 1}} } 29 | 30 | set viewpoints(4,0,1) { {{1 0 0 -22.703} {0 1 0 13.4484} {0 0 1 -12.2882} {0 0 0 1}} } 31 | 32 | set viewpoints(4,0,2) { {{0.0290998 0 0 0} {0 0.0290998 0 0} {0 0 0.0290998 0} {0 0 0 1}} } 33 | 34 | set viewpoints(4,0,3) { {{1 0 0 0.07} {0 1 0 0.03} {0 0 1 0} {0 0 0 1}} } 35 | 36 | set viewpoints(5,0,0) { {{0.965974 -0.0734215 0.247987 0} {-0.07252 0.843503 0.532205 0} {-0.248253 -0.532081 0.809479 0} {0 0 0 1}} } 37 | 38 | set viewpoints(5,0,1) { {{1 0 0 -22.703} {0 1 0 13.4484} {0 0 1 -12.2882} {0 0 0 1}} } 39 | 40 | set viewpoints(5,0,2) { {{0.0319271 0 0 0} {0 0.0319271 0 0} {0 0 0.0319271 0} {0 0 0 1}} } 41 | 42 | set viewpoints(5,0,3) { {{1 0 0 -0.04} {0 1 0 0.07} {0 0 1 0} {0 0 0 1}} } 43 | 44 | puts "\nLoaded viewpoints file viewpoints_01.tcl \n" 45 | 46 | -------------------------------------------------------------------------------- /Project/MovieBox/Movie/movie_script_01.tcl~: -------------------------------------------------------------------------------- 1 | move_vp_render 1 2 1 movie_frames ren_mov1 200 smooth 200 0; 2 | move_vp_render 2 2 201 movie_frames ren_mov1 200 smooth 0 200; 3 | mol showrep 0 0 off; 4 | move_vp_render 2 2 1 movie_frames ren_mov2 200 smooth 0 200; 5 | move_vp_render 2 3 201 movie_frames ren_mov2 200 smooth 200 200; 6 | mol showrep 0 1 off; 7 | mol showrep 0 2 off; 8 | move_vp_render 2 3 1 movie_frames ren_mov3 200 smooth 200 200; 9 | move_vp_render 3 3 201 movie_frames ren_mov3 200 smooth 200 350; 10 | move_vp_render 3 4 401 movie_frames ren_mov3 120 smooth 350 350; 11 | mol showrep 0 1 on; 12 | mol showrep 0 2 on; 13 | move_vp_render 3 4 1 movie_frames ren_mov4 120 smooth 350 350; 14 | move_vp_render 4 4 121 movie_frames ren_mov4 200 smooth 350 501; 15 | move_vp_render 4 5 321 movie_frames ren_mov4 200 smooth 501 501; 16 | 17 | 18 | 19 | -------------------------------------------------------------------------------- /Project/MovieBox/Scripts/.directory: -------------------------------------------------------------------------------- 1 | [Dolphin] 2 | AdditionalInfoV2=Details_Size,Details_Date,CustomizedDetails 3 | Timestamp=2012,4,16,14,4,57 4 | Version=2 5 | ViewMode=1 6 | -------------------------------------------------------------------------------- /Project/MovieBox/Scripts/local_render_tachyon: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ## 3 | ## local vmd render launching script April 2011 MikeK 4 | ## 5 | ## This script is designed to run a local version of vmd to render frames 6 | ## for molecular animations using tachyon. 7 | 8 | 9 | cd InBox; 10 | 11 | for i in * 12 | do 13 | if [ -f "$i" ]; then 14 | touch -f $i 15 | ## move file to Temp directory: 16 | 17 | mv $i ../Temp 18 | 19 | # modify file before processing: 20 | ## Tachyon Rendering Variables: 21 | 22 | sed 's/^Resolution.*/Resolution 1280 720/' ../Temp/$i >../Temp/temp.dat 23 | sed 's/^ Samples.*/ Samples 16/' ../Temp/temp.dat >../Temp/temp_file.dat 24 | 25 | ## render command: 26 | 27 | "/usr/local/lib/vmd/tachyon_LINUXAMD64" ../Temp/temp_file.dat -format TARGA -o ../Frames/$i.tga 28 | 29 | #tachyon -aasamples $aas -res $xres $yres ../Temp/$i -format TARGA -o ../Frames/$i.tga 30 | ## post rendering processing: 31 | 32 | ## move plot file to OutBox 33 | mv ../Temp/$i ../Outbox 34 | fi 35 | 36 | done 37 | 38 | #cleanup 39 | cd ../ 40 | mv *.e* Errors/ 41 | mv *.o* Output/ 42 | 43 | 44 | 45 | -------------------------------------------------------------------------------- /Project/MovieBox/Scripts/movie_script_example_01.tcl: -------------------------------------------------------------------------------- 1 | # Example movie script file. April 2012 MKuiper 2 | # 3 | # to use with view_change_render_2012_v1.tcl 4 | 5 | # After loading a scene in a tk console type: 6 | # play movie_script_01.tcl 7 | 8 | # new usage of move_vp_render: 9 | # move_vp_render start end first_frame_num dirName filePrefixName morph_frames start_frame end_frame transitions* 10 | # start - starting viewpoint 11 | # end - finishing viewpoint 12 | # first_frame_num - numbering of first frame 13 | # dirName - directory where to store tachyon .dat files. 14 | # filePrefixName - prefix of file name 15 | # morph_frames - how many frames in the transition between viewpoints 16 | # start_frame - first frame in dcd trajectory for this movie segment. 17 | # end_frame - last frame in dcd trajectory for this movie segment. 18 | # transitions* (optional) default: smooth 19 | # - can specify the type of transition between viewpoints with keywords: 20 | # smooth, sharp, smooth_start, smooth_end, tumble, and ninja 21 | 22 | move_vp_render 1 2 1 movie_frames movie_segment_1 200 200 0 smooth; 23 | move_vp_render 2 2 201 movie_frames movie_segment_1 200 0 200 sharp; 24 | 25 | # change rendering: 26 | mol showrep 0 0 off; 27 | 28 | move_vp_render 2 2 1 movie_frames movie_segment_2 200 0 200; 29 | move_vp_render 2 3 201 movie_frames movie_segment_2 200 200 200; 30 | 31 | mol showrep 0 1 off; 32 | mol showrep 0 2 off; 33 | 34 | move_vp_render 2 3 1 movie_frames movie_segment_3 200 200 200; 35 | 36 | 37 | 38 | -------------------------------------------------------------------------------- /Project/MovieBox/Scripts/old_scripts/.directory: -------------------------------------------------------------------------------- 1 | [Dolphin] 2 | AdditionalInfoV2=Details_Size,Details_Date,CustomizedDetails 3 | Timestamp=2012,4,16,14,5,15 4 | Version=2 5 | ViewMode=1 6 | -------------------------------------------------------------------------------- /Project/MovieBox/Scripts/pbs_render_tachyon: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ## 3 | ## PBS render launching script June 2013 MK 4 | ## 5 | ## -to run multiple rendering jobs, taking a plot file from Inbox, 6 | ## processing the image and moving the plot file to Outbox 7 | 8 | #PBS -l nodes=1:ppn=8 9 | #PBS -l walltime=24:0:0 10 | #PBS -A VR0012 11 | 12 | 13 | ## Tachyon Rendering Variables: 14 | set aas 8 # aasampling higher is better quality, but slower! 8 is usually good enough. 15 | set xres 1024 # x resolution - best to match with original input files 16 | set yres 768 # y resolution - best to match with original input files (ie 1024 x 768, 1900 x 1080 ) 17 | # set tachyon path: 18 | tachyon_path="/usr/local/vmd/1.9.1-gcc/lib/tachyon_LINUXAMD64" 19 | 20 | cd $PBS_O_WORKDIR 21 | module load vmd-gcc/1.9.1 22 | module load imagemagick 23 | 24 | cd Inbox; 25 | 26 | for i in * 27 | do 28 | if [ -f "$i" ]; then 29 | touch -f $i 30 | ## move file to Temp directory: 31 | mv $i ../Temp 32 | 33 | ## render command: 34 | 35 | $tachyon_path -aasamples $aas -res $xres $yres ../Temp/$i -format TARGA -o ../Frames/$i.tga 36 | 37 | ## post rendering processing: (optional!) 38 | # convert from tga format to jpg, remove old tga if successful. 39 | 40 | convert ../Frames/$i.tga ../Frames/$i.jpg 41 | 42 | if [ -f ../Frames/$i.jpg ]; 43 | then 44 | rm ../Frames/$i.tga 45 | fi 46 | 47 | 48 | ## move plot file to OutBox 49 | mv ../Temp/$i ../Outbox 50 | fi 51 | done 52 | 53 | #cleanup 54 | cd ../ 55 | mv *.e* Errors/ 56 | mv *.o* Output/ 57 | 58 | 59 | 60 | -------------------------------------------------------------------------------- /Project/MovieBox/Scripts/ppmconv: -------------------------------------------------------------------------------- 1 | # ppmconv: 2 | # this is a script to mass convert a pnm file to jpg. 3 | 4 | for pic in *.ppm 5 | do 6 | pnmtojpeg "${pic}" > "${pic/%ppm/jpg}" 7 | done 8 | 9 | -------------------------------------------------------------------------------- /Project/MovieBox/movie_script_example_01.tcl: -------------------------------------------------------------------------------- 1 | # Example movie script file. April 2012 MKuiper 2 | # 3 | # to use with view_change_render_2012_v1.tcl 4 | 5 | # After loading a scene in a tk console type: 6 | # play movie_script_01.tcl 7 | 8 | # new usage of move_vp_render: 9 | # move_vp_render start end first_frame_num dirName filePrefixName morph_frames start_frame end_frame transitions* 10 | # start - starting viewpoint 11 | # end - finishing viewpoint 12 | # first_frame_num - numbering of first frame 13 | # dirName - directory where to store tachyon .dat files. 14 | # filePrefixName - prefix of file name 15 | # morph_frames - how many frames in the transition between viewpoints 16 | # start_frame - first frame in dcd trajectory for this movie segment. 17 | # end_frame - last frame in dcd trajectory for this movie segment. 18 | # transitions* (optional) default: smooth 19 | # - can specify the type of transition between viewpoints with keywords: 20 | # smooth, sharp, smooth_start, smooth_end, tumble, and ninja 21 | 22 | move_vp_render 1 2 1 movie_frames movie_segment_1 200 200 0 smooth; 23 | move_vp_render 2 2 201 movie_frames movie_segment_1 200 0 200 sharp; 24 | 25 | # change rendering: 26 | mol showrep 0 0 off; 27 | 28 | move_vp_render 2 2 1 movie_frames movie_segment_2 200 0 200; 29 | move_vp_render 2 3 201 movie_frames movie_segment_2 200 200 200; 30 | 31 | mol showrep 0 1 off; 32 | mol showrep 0 2 off; 33 | 34 | move_vp_render 2 3 1 movie_frames movie_segment_3 200 200 200; 35 | 36 | 37 | 38 | -------------------------------------------------------------------------------- /Setup_and_Config/Benchmarking/BENCHMARK_SETUP.json: -------------------------------------------------------------------------------- 1 | { 2 | "Comment0" : "BENCHMARK setup file. Mar 2017", 3 | "Comment1" : "psf and pdb file should be found in /InputFiles", 4 | 5 | "PSFFILE" : "example.psf", 6 | "PDBFILE" : "example.pdb", 7 | 8 | "Comment2" : "Periodic boundary conditions dimensions:", 9 | "PBC_X" : "48", 10 | "PBC_Y" : "48", 11 | "PBC_Z" : "48", 12 | 13 | "ACCOUNT" : "VR0021", 14 | "NODELIST" : [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,22,24,26,30,32], 15 | "MODULEFILE" : "namd-intel/2.12", 16 | "RUNTIME" : "0:10:0", 17 | 18 | 19 | "Comment3" : "number of nodes for short equilibration run", 20 | "EquilNodes" : "8", 21 | 22 | 23 | "CustomFlag3" : 0 24 | 25 | } 26 | 27 | -------------------------------------------------------------------------------- /Setup_and_Config/Benchmarking/Benchmark_setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import sys 5 | import shutil 6 | import json 7 | import subprocess 8 | import fileinput 9 | from datetime import datetime 10 | 11 | 12 | """ A python script to help setup benchmarks runs on barcoo""" 13 | def read_benchmark_parameters(): 14 | """ Reads the json file 'BENCHMARK_SETUP.json' and 15 | returns the dictionary """ 16 | 17 | if os.path.isfile( 'BENCHMARK_SETUP.json' ): 18 | with open('BENCHMARK_SETUP.json') as json_data: 19 | bmp = json.load(json_data) 20 | json_data.close() 21 | return bmp 22 | else: 23 | print(("{}Can't see 'BENCHMARK_SETUP.json' {} "\ 24 | .format(RED, DEFAULT))) 25 | exit() 26 | 27 | def setup_benchmark(): 28 | """ Sets up initial benchmark files and launches job """ 29 | 30 | # read benchmark parameters: 31 | bmp = read_benchmark_parameters() 32 | psffile = bmp["PSFFILE"] 33 | pdbfile = bmp["PDBFILE"] 34 | pbcX = bmp["PBC_X"] 35 | pbcY = bmp["PBC_Y"] 36 | pbcZ = bmp["PBC_Z"] 37 | 38 | EqNode = bmp["EquilNodes"] 39 | account = bmp["ACCOUNT"] 40 | runtime = bmp["RUNTIME"] 41 | module = bmp["MODULEFILE"] 42 | 43 | # make equilibration config file. 44 | shutil.copy( 'Templates/namd_equilibration_script.template', 'namd_equilibration_script.conf') 45 | shutil.copy( 'Templates/sbatch_initial_benchmark.template', 'sbatch_initial_benchmark') 46 | 47 | for line in fileinput.FileInput( 'namd_equilibration_script.conf', inplace=True ): 48 | line = line.replace('XXX.psf', psffile) 49 | line = line.replace('XXX.pdb', pdbfile) 50 | line = line.replace('PBCX', pbcX) 51 | line = line.replace('PBCY', pbcY) 52 | line = line.replace('PBCZ', pbcZ) 53 | sys.stdout.write(line) 54 | 55 | for line in fileinput.FileInput( 'sbatch_initial_benchmark', inplace=True ): 56 | line = line.replace('XXXnode', EqNode) 57 | line = line.replace('XXXtime', runtime) 58 | line = line.replace('XXXmodule', module) 59 | line = line.replace('XXXaccount', account) 60 | sys.stdout.write(line) 61 | 62 | # launch equilibration job 63 | subprocess.Popen(['sbatch', 'sbatch_initial_benchmark']) 64 | 65 | if __name__ == "__main__": 66 | setup_benchmark() 67 | 68 | -------------------------------------------------------------------------------- /Setup_and_Config/Benchmarking/HOW_TO_RUN_BENCHMARKS.readme: -------------------------------------------------------------------------------- 1 | #---------------------------------------------------------------------------- 2 | How to run benchmarks. 3 | #---------------------------------------------------------------------------- 4 | 5 | ### WORK IN PROGRESS 6 | 7 | 8 | Benchmarking molecular dynamics jobs is useful to find the optimal sweetspot 9 | of speed and performance for a given node count. 10 | 11 | Hardware differences make it difficult to assume what optimal configurations 12 | are; it is far easier to run a short series of simulations with different 13 | numbers of nodes and plot the results. 14 | 15 | By running the same short job with different numbers of nodes, we can 16 | compare the relative performance. We typically find speed increases 17 | with more nodes but usually not linearly. At some point, the more nodes 18 | we use the significantly worse the performance gets. A common misconception 19 | people make is "more nodes is faster" - not strictly true! 20 | 21 | 22 | To run benchmarks we need to generate initial input from our files and 23 | then use that to runs a series of short jobs with different amounts of nodes. 24 | 25 | # Step 1. Generating initial benchmark starting points. 26 | #------------------------------------------------------------------------------ 27 | Edit the file: 28 | 29 | BENCHMARK_SETUP.json 30 | 31 | to list your input files and general setup parameters (such as account and nodelist). 32 | Next run the python benchmark setup script: 33 | ie) 34 | 35 | python Benchmark_setup.py 36 | 37 | 38 | This should generate some restart files which will be used in the benchmarking: 39 | bm_input.vel 40 | bm_input.coor 41 | bm_input.xsc 42 | bm_input.xst 43 | 44 | 45 | # Step 2. Run the benchmark set. 46 | #------------------------------------------------------------------------------ 47 | 48 | 49 | 50 | Edit the file: 51 | run_my_benchmarks.py 52 | 53 | To include a nodelist and account number, ie) 54 | nodelist = [1,2,4,8,16] 55 | account = "VR1234" 56 | 57 | - this example will benchmark using 1, 2, 4, 8, 16 nodes, using account number VR1234 58 | (make sure to use your own account) 59 | 60 | Launch the benchmarking jobs with: 61 | 62 | python run_my_benchmarks 63 | 64 | This will launch a series of jobs running with the number of nodes you specified. 65 | 66 | Raw timing output will be written to "raw_benchmark_data.txt" 67 | Which will give a list of 'nodes' and corresponding 'nanoseconds per day' and 'Nanoseconds per Node' 68 | the latter being a measure of efficiency. 69 | 70 | Generally, the more 'nanoseconds per day' the better, however not if the efficiency is 71 | terrible, as it is a poor use of resources. 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | -------------------------------------------------------------------------------- /Setup_and_Config/Benchmarking/Templates/bm_data_processing.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import sys 5 | 6 | """ A python script to help with post-processing of data of a MD simulation.""" 7 | 8 | outfile = sys.argv[1] 9 | 10 | timings = [] 11 | b= outfile.split('.') 12 | nodes = int(b[1]) 13 | 14 | # extracting timing data from the output file: 15 | def extract_timing_data(outfile): 16 | with open(outfile,"r") as f: 17 | for line in f: 18 | if 'Info: TIMESTEP' in line: # Find timestep information. 19 | ll = line.split() 20 | timestep = float(ll[2]) 21 | if 'TIMING:' in line: 22 | ll = line.split() 23 | timings.append(float(ll[4][:-5])) # Extract seconds per step, append to list. 24 | 25 | if (len(timings)>=3): # Take average of last 3 timings: 26 | ave = (timings[-1]+timings[-2]+timings[-3])/3.0 27 | 28 | # calulate nanoseconds per day 29 | nspd = 86400/ave * timestep /1000000.0 # Nanoseconds per day 30 | 31 | line = ( "%8.3f" % (nspd)) 32 | return line 33 | 34 | #def update_benchmarks(): 35 | 36 | 37 | def main(): 38 | # check outputfile exists. 39 | if os.path.isfile(outfile): 40 | timing= round((float(extract_timing_data(outfile))),3) 41 | eff = round((float(timing)/float(nodes)),3) 42 | line2 = str(nodes)+",\t"+str(timing)+",\t"+str(eff) 43 | with open("raw_benchmark_data.txt", "a") as f: 44 | f.write(line2) 45 | f.write("\n") 46 | f.close 47 | else: 48 | print "outputfile not found" 49 | 50 | if __name__ == "__main__": 51 | main() 52 | 53 | 54 | 55 | -------------------------------------------------------------------------------- /Setup_and_Config/Benchmarking/Templates/sbatch_benchmark_template: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ## sbatch benchmarking script template Jan 2015 MKuiper 3 | ## -A generic script to launch a series of benchmarking namd runs 4 | 5 | #-- Sbatch parameters:------------------------------------------ 6 | #-- the XXX values will be substituted from the run_mybenchamrk script 7 | 8 | #SBATCH --nodes=XXXnodes 9 | #SBATCH --time=XXXtime 10 | #SBATCH --account=XXXaccount 11 | 12 | module load XXXmodule # namd module file 13 | 14 | # submit benchmark job to the cluster:------------------------------------ 15 | 16 | srun namd2 generic_benchmark.conf >BenchmarkOutput.XXXnodes.out 2> BenchmarkOutput.XXXnodes.err; 17 | 18 | #--------------------------------------------------------------- 19 | # Process data: 20 | 21 | python Templates/bm_data_processing.py BenchmarkOutput.XXXnodes.out 22 | 23 | mv BenchmarkOutput.XXXnodes.* OLDRUNS/ 24 | mv slurm-$SLURM_JOBID.out OLDRUNS/ 25 | 26 | -------------------------------------------------------------------------------- /Setup_and_Config/Benchmarking/Templates/sbatch_initial_benchmark.template: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ## sbatch initial benchmark setup Mar 2017 MKuiper 3 | ## 4 | ## Simple sbatch script to launch the initial short equilibration script, 5 | ## -designed to generate input restart files for the benchmarking runs. 6 | ## 7 | 8 | 9 | #SBATCH --nodes=XXXnode 10 | #SBATCH --time=XXXtime 11 | #SBATCH --account=XXXaccount 12 | 13 | module load XXXmodule 14 | 15 | 16 | # submit to the cluster:------------------------------------ 17 | 18 | srun namd2 namd_equilibration_script.conf >temp_working_outputfile.out 2> temp_working_errorsfile.err; 19 | 20 | #--------------------------------------------------------------- 21 | # clean up: 22 | 23 | rm namd_equilibration_script.conf 24 | rm sbatch_initial_benchmark 25 | mv slurm-$SLURM_JOBID.out OLDRUNS/ 26 | mv temp_working_outputfile.* OLDRUNS/ 27 | 28 | -------------------------------------------------------------------------------- /Setup_and_Config/Benchmarking/raw_benchmark_data.txt: -------------------------------------------------------------------------------- 1 | Starting new benchmark run: 04:04:2017 15:29 2 | Nodes ns/day ns/node (ns- nanoseconds) 3 | 26, 35.775, 1.376 4 | 24, 33.693, 1.404 5 | 22, 31.65, 1.439 6 | 20, 29.417, 1.471 7 | 19, 25.354, 1.334 8 | 18, 24.213, 1.345 9 | 17, 23.438, 1.379 10 | 16, 22.958, 1.435 11 | 15, 22.392, 1.493 12 | 14, 20.496, 1.464 13 | 30, 39.959, 1.332 14 | 13, 19.419, 1.494 15 | 12, 18.026, 1.502 16 | 11, 16.535, 1.503 17 | 10, 15.401, 1.54 18 | 9, 14.184, 1.576 19 | 32, 42.174, 1.318 20 | 8, 12.878, 1.61 21 | 7, 11.208, 1.601 22 | 6, 9.677, 1.613 23 | 5, 8.477, 1.695 24 | 4, 6.939, 1.735 25 | 3, 5.191, 1.73 26 | 2, 3.576, 1.788 27 | 1, 1.832, 1.832 28 | -------------------------------------------------------------------------------- /Setup_and_Config/Benchmarking/run_my_benchmarks.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import sys 5 | import shutil 6 | import json 7 | import subprocess 8 | import fileinput 9 | from datetime import datetime 10 | from Benchmark_setup import read_benchmark_parameters 11 | 12 | """ A python script to help run benchmarking runs on barcoo""" 13 | def run_benchmark(): 14 | # check if input files exists. 15 | if not os.path.exists("bm_input.coor"): 16 | print("Input files not found. Have you run the benchmark setup to generate input files? \n(python Benchmark_setup.py)") 17 | exit() 18 | 19 | # read benchmark parameters: 20 | bmp = read_benchmark_parameters() 21 | nodelist = bmp["NODELIST"] 22 | account = bmp["ACCOUNT"] 23 | runtime = bmp["RUNTIME"] 24 | module = bmp["MODULEFILE"] 25 | 26 | date = datetime.now().strftime("%d:%m:%Y %H:%M ") 27 | p = "Starting new benchmark run: " + date + "\nNodes \tns/day\tns/node (ns- nanoseconds)" 28 | with open("raw_benchmark_data.txt", "w") as f: 29 | f.write(p) 30 | f.write("\n") 31 | f.close 32 | 33 | for i in nodelist: 34 | bm_script = write_benchmark_config(i, account, runtime, module) 35 | subprocess.Popen(['sbatch', bm_script]) 36 | 37 | def write_benchmark_config(i, account, runtime, module): 38 | '''simple script to substitute values into benchmarking config script''' 39 | 40 | bm_name = 'bm_config.' + str(i) + '.sbatch' 41 | name = bm_name 42 | shutil.copy( 'Templates/sbatch_benchmark_template', 'temp_bm_config') 43 | 44 | for line in fileinput.FileInput( 'temp_bm_config', inplace=True ): 45 | line = line.replace('XXXnodes', str(i) ) 46 | line = line.replace('XXXaccount', account) 47 | line = line.replace('XXXtime', runtime) 48 | line = line.replace('XXXmodule', module) 49 | sys.stdout.write(line) 50 | 51 | shutil.copy( 'temp_bm_config', bm_name ) 52 | os.remove('temp_bm_config') 53 | return name 54 | 55 | if __name__ == "__main__": 56 | run_benchmark() 57 | 58 | -------------------------------------------------------------------------------- /Setup_and_Config/JobTemplate/Errors/.gitignore: -------------------------------------------------------------------------------- 1 | # Ignore everything in this directory 2 | * 3 | # Except this file 4 | !.gitignore 5 | -------------------------------------------------------------------------------- /Setup_and_Config/JobTemplate/JobLog/.gitignore: -------------------------------------------------------------------------------- 1 | # Ignore everything in this directory 2 | * 3 | # Except this file 4 | !.gitignore 5 | -------------------------------------------------------------------------------- /Setup_and_Config/JobTemplate/LastRestart/.gitignore: -------------------------------------------------------------------------------- 1 | # Ignore everything in this directory 2 | * 3 | # Except this file 4 | !.gitignore 5 | -------------------------------------------------------------------------------- /Setup_and_Config/JobTemplate/OutputFiles/.gitignore: -------------------------------------------------------------------------------- 1 | # Ignore everything in this directory 2 | * 3 | # Except this file 4 | !.gitignore 5 | -------------------------------------------------------------------------------- /Setup_and_Config/JobTemplate/OutputText/.gitignore: -------------------------------------------------------------------------------- 1 | # Ignore everything in this directory 2 | * 3 | # Except this file 4 | !.gitignore 5 | -------------------------------------------------------------------------------- /Setup_and_Config/JobTemplate/RestartFiles/.gitignore: -------------------------------------------------------------------------------- 1 | # Ignore everything in this directory 2 | * 3 | # Except this file 4 | !.gitignore 5 | -------------------------------------------------------------------------------- /Setup_and_Config/MolecularSoup/sbatch_production_script.template: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ## sbatch launching script template Sept 2017 MKuiper 3 | ## -A generic script to launch a series of production namd runs 4 | #--------------------------------------------------------------- 5 | # Make all changes in "master_config_file" # 6 | # -you shouldn't have to change anything in here! # 7 | #--------------------------------------------------------------- 8 | #-- Sbatch parameters:------------------------------------------ 9 | #-- the X values will be substituted with a values from the master_config_file 10 | #-- when you populate job directories with ./mdwf -p 11 | 12 | #SBATCH --nodes=X 13 | #SBATCH --time=X 14 | #SBATCH --tasks-per-node=X 15 | #SBATCH --gres gpu:X 16 | 17 | production_script=X 18 | 19 | module load openmpi 20 | module load X # module file 21 | 22 | 23 | NNODE=$SLURM_JOB_NUM_NODES 24 | NTASKS=$SLURM_NTASKS_PER_NODE 25 | 26 | # calculate total processes (P) and processes per node (PPN) (for multinode jobs) 27 | PPN=`expr $SLURM_NTASK_PER_NODE - 1` 28 | P="$(($PPN * $SLURM_NNODES))" 29 | 30 | # GPUS=" +idlepoll +devices $CUDA_VISIBLE_DEVICES" <- this seems to cause troulbe with GPU allocation 31 | GPUS=" +idlepoll " 32 | 33 | # For trouble shooting: 34 | echo "cuda devices: production" >> cuda.info 35 | echo $CUDA_VISIBLE_DEVICES >> cuda.info 36 | echo $GPUS >> cuda.info 37 | nvidia-smi >> cuda.info 38 | 39 | # update current configuration files from above directory. 40 | cp ../*.py . 41 | cp ../namd* . 42 | 43 | scontrol show job $SLURM_JOBID >>scontrol.info 44 | #-------------------------------------------------------------------------------------------- 45 | # python script for preprocessing data 46 | if [ -f ../prejob_processing.py ]; 47 | then python3 ../prejob_processing.py $SLURM_JOBID -production; 48 | else echo "No processing script" > pausejob 49 | fi 50 | 51 | # prevent job from running if pausejob is present 52 | if [ -f pausejob ]; then exit; fi 53 | 54 | # run production job: 55 | if [ $NNODE == 1 ]; then 56 | 57 | namd2 +ppn $NTASKS $GPUS $production_script >temp_working_outputfile.out 2>temp_working_errorsfile.err; 58 | # namd2 +ppn $NTASKS +idlepoll +devices 0 $production_script >temp_working_outputfile.out 2>temp_working_errorsfile.err; 59 | fi 60 | 61 | #-------------------------------------------------------------------------------------------- 62 | # python script for postprocessing data 63 | if [ -f ../postjob_processing.py ]; 64 | then python3 ../postjob_processing.py $SLURM_JOBID -production; 65 | else echo "No processing script" > pausejob 66 | fi 67 | 68 | # prevent job from running if pausejob is present 69 | if [ -f pausejob ]; then 70 | exit 71 | fi 72 | 73 | # launch next job: 74 | 75 | sbatch sbatch_production_script 76 | 77 | -------------------------------------------------------------------------------- /Setup_and_Config/MolecularSoup/sbatch_production_script.template.mpi: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # Bracewell NAMD script. 4 | 5 | # Original Author: Tim Ho modified by Mike Kuiper 6 | # Support: contact schelp@csiro.au 7 | 8 | # Slurm variables: 9 | #-------------------------------------------------------------- 10 | #SBATCH --nodes 2 11 | #SBATCH --tasks-per-node 28 12 | #SBATCH --gres gpu:2 13 | #SBATCH --time=2:0:0 14 | 15 | CONFIG=namd_production_script.conf 16 | 17 | # Modules 18 | #-------------------------------------------------------------- 19 | module load openmpi 20 | module load namd/2.12-ibverbs-smp-cuda 21 | 22 | # Job variables: 23 | #-------------------------------------------------------------- 24 | NNODE=$SLURM_JOB_NUM_NODES 25 | NTASKS=$SLURM_NTASKS_PER_NODE 26 | 27 | GPUS="" 28 | if [ "$CUDA_VISIBLE_DEVICES" != "" ] 29 | then 30 | GPUS="+idlepoll +devices $CUDA_VISIBLE_DEVICES" 31 | fi 32 | 33 | # Logging data: 34 | #-------------------------------------------------------------- 35 | echo $GPUS >> cuda.info 36 | echo nvidia-smi >> cuda.info 37 | scontrol show job $SLURM_JOBID >>scontrol.info 38 | 39 | # Pre-processing script: 40 | #-------------------------------------------------------------- 41 | if [ -f ../prejob_processing.py ]; 42 | then python3 ../prejob_processing.py $SLURM_JOBID -production; 43 | else echo "No pre-processing script." > pausejob 44 | fi 45 | 46 | # Runaway checkpoint: 47 | #-------------------------------------------------------------- 48 | if [ -f pausejob ]; then 49 | scancel $SLURM_JOBID; 50 | exit; 51 | fi 52 | 53 | # Launching job: 54 | #-------------------------------------------------------------- 55 | if [ $NNODE == 1 ] 56 | then 57 | # Single-node SMP 58 | namd2 ++ppn $NTASKS $GPUS "$CONFIG" >temp_working_outputfile.out 2>temp_working_errorsfile.err; 59 | 60 | else 61 | # Multi-node SMP via MPI 62 | # PPN=`expr $SLURM_NTASKS_PER_NODE - 1 ` # <- usually one core reserved for comms. 63 | PPN=`expr $SLURM_NTASKS_PER_NODE - 0 ` 64 | P="$(($PPN * $SLURM_NNODES))" 65 | 66 | charmrun ++verbose ++mpiexec \ 67 | ++remote-shell "`which mpirun` --map-by node" \ 68 | `which namd2` ++p $P ++ppn $PPN +setcpuaffinity $GPUS \ 69 | "$CONFIG" >temp_working_outputfile.out 2>temp_working_errorsfile.err; 70 | fi 71 | 72 | # Post-processing script: 73 | #-------------------------------------------------------------- 74 | if [ -f ../postjob_processing.py ]; 75 | then python3 ../postjob_processing.py $SLURM_JOBID -production; 76 | else echo "No post-processing script." > pausejob 77 | fi 78 | 79 | # Runaway checkpoint: 80 | #-------------------------------------------------------------- 81 | if [ -f pausejob ]; then 82 | scancel $SLURM_JOBID; 83 | exit; 84 | fi 85 | 86 | # Launch nextjob: 87 | #-------------------------------------------------------------- 88 | sbatch sbatch_production_script 89 | 90 | 91 | -------------------------------------------------------------------------------- /Setup_and_Config/job_details_template.json: -------------------------------------------------------------------------------- 1 | { 2 | "Comment0" : "Job_details_json_file v0.5", 3 | 4 | "BASE_DIR" : "unassigned", 5 | "JOB_STREAM_DIR" : "unassigned", 6 | "JobDirName" : "unassigned", 7 | "JobBaseName" : "unassigned", 8 | 9 | "Comment1" : "Job details", 10 | "Account" : "unassigned", 11 | "ResourceManager" : "slurm", 12 | 13 | "CurrentJobId" : 0, 14 | "QueueStatus" : "not started", 15 | "JobStatus" : "ready", 16 | "JobMessage" : "not started", 17 | "ErrorsMessages" : 0, 18 | "Nodes" : 0, 19 | "NodeList" : 0, 20 | "GPUsList" : 0, 21 | "Walltime" : 0, 22 | 23 | "CurrentRun" : 0, 24 | "TotalRuns" : 0, 25 | 26 | "PauseJobFlag" : 0, 27 | "LastTimingValue": 0, 28 | "OldSlurmFileID" : 0, 29 | "LastJobId" : 0, 30 | "JobStartTime" : 0, 31 | "JobFinishTime" : 0, 32 | "JobFailTime" : 0, 33 | "DiskSpaceCutOff": 0, 34 | 35 | "CustomFlag1" : 0, 36 | "CustomFlag2" : 0, 37 | "CustomFlag3" : 0 38 | 39 | } 40 | 41 | -------------------------------------------------------------------------------- /Setup_and_Config/local_job_details_template.json: -------------------------------------------------------------------------------- 1 | { 2 | "Comment0" : "Job_details_json_file v0.5", 3 | 4 | "BASE_DIR" : "unassigned", 5 | "JOB_STREAM_DIR" : "unassigned", 6 | "JobDirName" : "unassigned", 7 | "JobBaseName" : "unassigned", 8 | "==----------==" : "---------------", 9 | "Account" : "unassigned", 10 | "Nodes" : 0, 11 | "GPUs" : 0, 12 | "Walltime" : 0, 13 | "CurrentJobId" : 0, 14 | "LastJobId" : 0, 15 | "====------====" : "----------------", 16 | "CurrentRun" : 0, 17 | "TotalRuns" : 0, 18 | "=-=-=-=-=-=-=-" : "----------------", 19 | "QueueStatus" : "not started", 20 | "JobStatus" : "ready", 21 | "JobMessage" : "not started", 22 | "ErrorsMessages" : 0, 23 | "PauseJobFlag" : 0, 24 | "==============" : "----------------", 25 | "JobStartTime" : 0, 26 | "JobFinishTime" : 0, 27 | "JobFailTime" : 0, 28 | "--==========--" : "----------------", 29 | "CustomFlag1" : 0, 30 | "CustomFlag2" : 0, 31 | "CustomFlag3" : 0 32 | 33 | } 34 | 35 | -------------------------------------------------------------------------------- /Setup_and_Config/postjob_processing.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python3 2 | 3 | import os 4 | import sys 5 | import time 6 | lib_path = os.path.abspath('../../mdwf_lib') 7 | sys.path.append(lib_path) 8 | import mdwf_functions as mdwf 9 | 10 | """ A python script to help with post-processing of data of a MD simulation.""" 11 | 12 | jobid = sys.argv[1] 13 | jobtype = sys.argv[2] 14 | 15 | 16 | ## generic name of working MD files, (must be the same in .conf files). 17 | filename = "current_MD_run_files" 18 | 19 | def main(): 20 | ## update local job details file: 21 | mdwf.update_local_job_details("JobFinishTime", time.time()) 22 | mdwf.check_job_runtime() 23 | 24 | timestamp = "Finished: " + time.strftime("%d%b:%H:%M", time.localtime()) 25 | mdwf.update_local_job_details("JobMessage", timestamp) 26 | mdwf.update_local_job_details("JobStatus", "stopped") 27 | 28 | mdwf.redirect_namd_output(filename, jobtype) # -redirect output 29 | mdwf.check_run_counter("post") # -check job counter 30 | mdwf.post_jobrun_cleanup() # -cleanup files 31 | 32 | if __name__ == "__main__": 33 | main() 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /Setup_and_Config/prejob_processing.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python3 2 | 3 | import os 4 | import sys 5 | import time 6 | lib_path = os.path.abspath('../../mdwf_lib') 7 | sys.path.append(lib_path) 8 | import mdwf_functions as mdwf 9 | 10 | """ A python script to help do the data pre-processing before submitting the job.""" 11 | 12 | jobid = sys.argv[1] # job id of submitted job. 13 | jobtype = sys.argv[2] # job type, 14 | 15 | def main(): 16 | 17 | ## performs checks before launching the job: 18 | mdwf.check_run_counter("pre") # -check job counter 19 | mdwf.check_pausejob_flag() # -checks for pausejob flag 20 | 21 | ## update the local job details file: 22 | mdwf.update_local_job_details( "CurrentJobId", jobid ) 23 | mdwf.update_local_job_details( "JobStatus", "running" ) 24 | 25 | timestamp = "Started: " + time.strftime( "%d%b:%H:%M", time.localtime() ) 26 | mdwf.update_local_job_details( "JobMessage", timestamp ) 27 | mdwf.update_local_job_details( "JobStartTime", time.time()) 28 | 29 | if __name__ == "__main__": 30 | main() 31 | 32 | -------------------------------------------------------------------------------- /Setup_and_Config/readme.txt: -------------------------------------------------------------------------------- 1 | /Setup_and_Config directory notes. 2 | 3 | The purpose of the /Setup_and_Config directory is to setup the 4 | design and workflow of your experiment. Though this was developed with 5 | molecular dynamics in mind, it could be adapted to run and manage any 6 | number of programs. 7 | 8 | There are 2 python scripts to do pre-processing and post-processing of the 9 | data which are specific to the NAMD workflow. These could be modified for any 10 | program. 11 | 12 | This directory structure has a number of template files which are copied 13 | and modified when the 'populate' flag is used in the top directory ie) 14 | ./mdwf -p 15 | This is defined in /mdwf_lib/mdwf_functions.py 16 | 17 | -------------------------------------------------------------------------------- /Setup_and_Config/sbatch_production_script.template.mpi: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # Bracewell NAMD script. 4 | 5 | # Original Author: Tim Ho modified by Mike Kuiper 6 | # Support: contact schelp@csiro.au 7 | 8 | # Slurm variables: 9 | #-------------------------------------------------------------- 10 | #SBATCH --nodes 2 11 | #SBATCH --tasks-per-node 28 12 | #SBATCH --gres gpu:2 13 | #SBATCH --time=2:0:0 14 | 15 | CONFIG=namd_production_script.conf 16 | 17 | # Modules 18 | #-------------------------------------------------------------- 19 | module load openmpi 20 | module load namd/2.12-ibverbs-smp-cuda 21 | 22 | # Job variables: 23 | #-------------------------------------------------------------- 24 | NNODE=$SLURM_JOB_NUM_NODES 25 | NTASKS=$SLURM_NTASKS_PER_NODE 26 | 27 | GPUS="" 28 | if [ "$CUDA_VISIBLE_DEVICES" != "" ] 29 | then 30 | GPUS="+idlepoll +devices $CUDA_VISIBLE_DEVICES" 31 | fi 32 | 33 | # Logging data: 34 | #-------------------------------------------------------------- 35 | echo $GPUS >> cuda.info 36 | echo nvidia-smi >> cuda.info 37 | scontrol show job $SLURM_JOBID >>scontrol.info 38 | 39 | # Pre-processing script: 40 | #-------------------------------------------------------------- 41 | if [ -f ../prejob_processing.py ]; 42 | then python3 ../prejob_processing.py $SLURM_JOBID -production; 43 | else echo "No pre-processing script." > pausejob 44 | fi 45 | 46 | # Runaway checkpoint: 47 | #-------------------------------------------------------------- 48 | if [ -f pausejob ]; then 49 | scancel $SLURM_JOBID; 50 | exit; 51 | fi 52 | 53 | # Launching job: 54 | #-------------------------------------------------------------- 55 | if [ $NNODE == 1 ] 56 | then 57 | # Single-node SMP 58 | namd2 ++ppn $NTASKS $GPUS "$CONFIG" >temp_working_outputfile.out 2>temp_working_errorsfile.err; 59 | 60 | else 61 | # Multi-node SMP via MPI 62 | # PPN=`expr $SLURM_NTASKS_PER_NODE - 1 ` # <- usually one core reserved for comms. 63 | PPN=`expr $SLURM_NTASKS_PER_NODE - 0 ` 64 | P="$(($PPN * $SLURM_NNODES))" 65 | 66 | charmrun ++verbose ++mpiexec \ 67 | ++remote-shell "`which mpirun` --map-by node" \ 68 | `which namd2` ++p $P ++ppn $PPN +setcpuaffinity $GPUS \ 69 | "$CONFIG" >temp_working_outputfile.out 2>temp_working_errorsfile.err; 70 | fi 71 | 72 | # Post-processing script: 73 | #-------------------------------------------------------------- 74 | if [ -f ../postjob_processing.py ]; 75 | then python3 ../postjob_processing.py $SLURM_JOBID -production; 76 | else echo "No post-processing script." > pausejob 77 | fi 78 | 79 | # Runaway checkpoint: 80 | #-------------------------------------------------------------- 81 | if [ -f pausejob ]; then 82 | scancel $SLURM_JOBID; 83 | exit; 84 | fi 85 | 86 | # Launch nextjob: 87 | #-------------------------------------------------------------- 88 | sbatch sbatch_production_script 89 | 90 | 91 | -------------------------------------------------------------------------------- /function_files.txt: -------------------------------------------------------------------------------- 1 | 2 | # read functions: 3 | def read_master_config_file(): 4 | def read_local_job_details(path="Setup_and_Config", 5 | def read_namd_job_details(targetfile): 6 | 7 | 8 | 9 | def gather_jobs(): 10 | def gather_list(): 11 | def extend_jobs(a): 12 | def extend_runs(a): 13 | def get_atoms(psffile): 14 | def pausejob_flag( directive ): 15 | def check_pausejob_flag(): 16 | def check_disk_quota(): 17 | def log_job_details( jobid ): 18 | def check_job_runtime(): 19 | If the run time is less than a certain cutoff defined in the 20 | def check_run_counter(processing="post"): 21 | def cleanup_job_runs(): 22 | def get_job_runtime( starttime, status ): 23 | def create_job_basename( jobname, run, zf ): 24 | def update_local_job_details( key, status ): 25 | def redirect_namd_output( CurrentWorkingName = "current_MD_run_files", 26 | def post_jobrun_cleanup(): 27 | def update_local_dcd_list(): 28 | def final_job_cleanup(): 29 | def log_job_timing(): 30 | def countdown_timer(): 31 | def check_if_job_running(): 32 | def monitor_jobs(): 33 | def md5sum( filename, blocksize=65536 ): 34 | def getfilesize( filename ): 35 | def check_job_structure(): 36 | def initialize_job_directories(): 37 | as defined in the 'master_config_file'. This function copies 38 | def populate_job_directories(): 39 | def check_job(): 40 | def check_file_exists(target): 41 | def benchmark(): 42 | def get_current_dir_list(job_dir): 43 | def get_current_file_list(job_dir): 44 | def execute_function_in_job_tree( func, *args ): 45 | def start_all_jobs(): 46 | def start_jobs( startscript ): 47 | def clear_jobs(): 48 | def clear_all_jobs(): 49 | def restart_all_production_jobs(): 50 | def restart_jobs(restart_script): 51 | def recover_all_jobs(): 52 | def recovery_function(): 53 | def stop_jobs(): 54 | def pause_jobs(): 55 | def pause_all_jobs(): 56 | def stop_all_jobs_immediately(): 57 | def erase_all_data(): 58 | def create_dcd_file_loader( first = 0, last = -1, step =1): 59 | def clone(): 60 | -------------------------------------------------------------------------------- /master_config_file: -------------------------------------------------------------------------------- 1 | { 2 | "Comment0" : "Master_Config_File v0.5", 3 | "Account" : "AccountNo", 4 | "Flavour" : "Namd", 5 | "UserName" : "anonymous", 6 | "Walltime" : "2:0:0", 7 | "Nodes" : "1", 8 | "TaskPerNode" : "28", 9 | "GPUsPerNode" : "1", 10 | "O2D" : "OD-change_me", 11 | 12 | "ModuleFile" : "namd/2.14-verbs-smp-cuda", 13 | "MPIModule" : "blank", 14 | "PsfFileName" : "ChangeMe.psf", 15 | "PdbFileName" : "ChangeMe.pdb", 16 | 17 | "Comment1" : "Job Details Section", 18 | 19 | "JobStreams" : ["MainJobDir_01"], 20 | "JobReplicates" : ["2"], 21 | "BaseDirNames" : ["Sim1_"], 22 | "JobBaseNames" : ["sim_"], 23 | "Runs" : ["5" ], 24 | 25 | "JobScheme" : "simple", 26 | "Round" : 1, 27 | 28 | "SbatchEquilibrateScript" : "sbatch_start_script", 29 | "EquilibrateConfScript" : "namd_equilibration_script.conf", 30 | 31 | "SbatchProductionScript" : "sbatch_production_script", 32 | "ProductionConfScript" : "namd_production_script.conf", 33 | 34 | "custom_script1" : "custom1.conf", 35 | "custom_script2" : "custom2.conf", 36 | 37 | "Comment2" : "Miscellaneous Parameters", 38 | 39 | "JobFailTime" : 20, 40 | "DiskSpaceCutOff" : 95, 41 | "AutoAnalysis" : "False" 42 | 43 | } 44 | -------------------------------------------------------------------------------- /mdwf_lib/.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *.pyc 5 | 6 | # Specific to MD_workflow 7 | Main_Job_Dir/ 8 | 9 | # C extensions 10 | *.so 11 | 12 | # Distribution / packaging 13 | .Python 14 | env/ 15 | bin/ 16 | build/ 17 | develop-eggs/ 18 | dist/ 19 | eggs/ 20 | lib/ 21 | lib64/ 22 | parts/ 23 | sdist/ 24 | var/ 25 | *.egg-info/ 26 | .installed.cfg 27 | *.egg 28 | 29 | # Installer logs 30 | pip-log.txt 31 | pip-delete-this-directory.txt 32 | 33 | # Unit test / coverage reports 34 | htmlcov/ 35 | .tox/ 36 | .coverage 37 | .cache 38 | nosetests.xml 39 | coverage.xml 40 | 41 | # Translations 42 | *.mo 43 | 44 | # Mr Developer 45 | .mr.developer.cfg 46 | .project 47 | .pydevproject 48 | 49 | # Rope 50 | .ropeproject 51 | 52 | # Django stuff: 53 | *.log 54 | *.pot 55 | 56 | # Sphinx documentation 57 | docs/_build/ 58 | -------------------------------------------------------------------------------- /mdwf_lib/AvocaLegacyCode/master_config_file: -------------------------------------------------------------------------------- 1 | { 2 | "Comment0" : "Master_Config_File v0.25", 3 | "Account" : "VR0002", 4 | "Flavour" : "Namd", 5 | "UserName" : "mike", 6 | 7 | "Comment1" : "BlueGene/Q Namd Job parameters:", 8 | "nodes" : "1", 9 | "ntpn" : "8", 10 | "ppn" : "8", 11 | "Walltime" : "2:0:0", 12 | 13 | "ModuleFile" :"namd-xl-pami-smp/2.10", 14 | "PsfFileName" : "ChangeMe.psf", 15 | "PdbFileName" : "ChangeMe.pdb", 16 | 17 | 18 | "Comment2" : "Job Details Section", 19 | "JobStreams" : ["MainJobdir1"], 20 | "JobReplicates" : ["5"], 21 | "BaseDirNames" : ["Sim1_" ], 22 | "JobBaseNames" : ["MyJob1_" ], 23 | "Runs" : ["5" ], 24 | 25 | "JobScheme" : "simple", 26 | "Round" : 1, 27 | 28 | "SbatchEquilibrateScript" : "sbatch_start_script", 29 | "EquilibrateConfScript" : "namd_equilibration_script.conf", 30 | 31 | "SbatchProductionScript" : "sbatch_production_script", 32 | "ProductionConfScript" : "namd_production_script.conf", 33 | 34 | "custom_script1" : "custom1.conf", 35 | "custom_script2" : "custom2.conf", 36 | 37 | "Comment4" : "Miscellaneous Parameters", 38 | "JobFailTime" : 60, 39 | "DiskSpaceCutOff" : 95, 40 | "AutoAnalysis" : "False" 41 | 42 | } 43 | -------------------------------------------------------------------------------- /mdwf_lib/__init__.py: -------------------------------------------------------------------------------- 1 | #!/usr/local/python/3.6.0-gcc/bin/python3 2 | 3 | -------------------------------------------------------------------------------- /mdwf_lib/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mkuiper/MD_workflow_py/08803104d805f52b2065ef18b33fc739a68e1036/mdwf_lib/__init__.pyc -------------------------------------------------------------------------------- /mdwf_lib/readme.txt: -------------------------------------------------------------------------------- 1 | # /bin directory. 2 | # 3 | # local directory for storage of executables and python modules. 4 | 5 | -------------------------------------------------------------------------------- /project_plan.txt: -------------------------------------------------------------------------------- 1 | #------------------------------------------------------------------------------| 2 | # Project Planning: March 2017 | 3 | |------------------------------------------------------------------------------| 4 | | This document is designed to help the user properly plan their molecular | 5 | | dynamics experiments. We encourage users to fill this out prior to a | 6 | | MD experiment, to both justify the rationale and also keep a record for | 7 | | future reference. Remember, any experiment that is not written up or used | 8 | | in future work may as well not been run at all. | 9 | | | 10 | | To aid this process we'll borrow from 'Heilmeier's catechisms' | 11 | #------------------------------------------------------------------------------| 12 | Date: 13 | 14 | Project title: 15 | 16 | Members: 17 | 18 | VLSCI Project: 19 | 20 | #-Heilmeier-catechisms---------------------------------------------------------| 21 | 1) What are you trying to do? 22 | 23 | 2) How is it done today, and what are the limits of current practice? 24 | 25 | 3) What's new in your approach and why do you think it will be successful? 26 | 27 | 4) Who cares? 28 | 29 | 5) If you're successful, what difference will it make? 30 | 31 | 6) What are the risks and the payoffs? 32 | 33 | 7) How much will it cost? 34 | 35 | 8) How long will it take? 36 | 37 | 9) What are the midterm and final indicators to check for success? 38 | 39 | 40 | # Experimental Design: 41 | #------------------------------------------------------------------------------| 42 | 43 | Equilibrium stage? 44 | 45 | Size /temperature? 46 | 47 | Ensemble. NVT / NPT? 48 | 49 | Temperature control? 50 | 51 | Pressure control? 52 | 53 | Statistical sampling? 54 | 55 | Analysis? What will you measure from this? 56 | 57 | What figures or representation can you make from the results? Is this 58 | work going result in a publication? 59 | 60 | What journal might you hope this work to be published in. 61 | 62 | 63 | 64 | 65 | 66 | -------------------------------------------------------------------------------- /sbatch_backup_script: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ## sbatch script to backup directories Aug 2021 MKuiper 3 | 4 | #SBATCH --nodes=1 5 | #SBATCH --time=12:0:0 6 | #SBATCH --tasks-per-node=4 7 | 8 | # clean up git files if present. 9 | # rm -rf .git 10 | # find . -name .gitkeep -type f -delete 11 | 12 | dir="directory name -change me" 13 | 14 | TODAY="$(date +%d-%m-%Y)" 15 | 16 | # Create a local copy of the directory: 17 | tar -zcvf $dir.$TODAY.tar.gz $dir 18 | 19 | # Move tar archive to store dir. 20 | mv $dir.$TODAY.tar.gz $STOREDIR/ 21 | 22 | #-------------------------------------------------------------------------------- 23 | 24 | 25 | --------------------------------------------------------------------------------