├── README.md ├── docs └── python-libs.tex ├── examples ├── CGenFF │ ├── N-methylacetamide │ │ ├── LIG_ffbonded.itp │ │ ├── after_cg.g96 │ │ ├── conf.gro │ │ ├── eigenfreq.xvg │ │ ├── eigenval.xvg │ │ ├── eigenvec.trr │ │ ├── ener.edr │ │ ├── mdout.mdp │ │ ├── minimize.log │ │ ├── minimize.tpr │ │ ├── nm.log │ │ ├── nm.mtx │ │ ├── nm.tpr │ │ ├── old.top │ │ ├── output │ │ ├── topol.top │ │ └── traj.trr │ ├── charmm36.ff │ │ ├── atomtypes.atp │ │ ├── bugs │ │ ├── cmap.itp │ │ ├── ffbonded.itp │ │ ├── ffnonbonded.itp │ │ ├── forcefield.doc │ │ ├── forcefield.itp │ │ ├── gb.itp │ │ ├── hack.itp │ │ ├── ions.itp │ │ ├── merged.arn │ │ ├── merged.c.tdb │ │ ├── merged.hdb │ │ ├── merged.n.tdb │ │ ├── merged.r2b │ │ ├── merged.rtp │ │ ├── merged.vsd │ │ ├── mol │ │ │ ├── aald.itp │ │ │ ├── aald.pdb │ │ │ ├── acet.itp │ │ │ ├── acet.pdb │ │ │ ├── acey.itp │ │ │ ├── acey.pdb │ │ │ ├── acox.itp │ │ │ ├── acox.pdb │ │ │ ├── anil.itp │ │ │ ├── anil.pdb │ │ │ ├── benx.itp │ │ │ ├── benx.pdb │ │ │ ├── benz.itp │ │ │ ├── benz.pdb │ │ │ ├── brob.itp │ │ │ ├── brob.pdb │ │ │ ├── chlb.itp │ │ │ ├── chlb.pdb │ │ │ ├── flub.itp │ │ │ ├── flub.pdb │ │ │ ├── form.itp │ │ │ ├── form.pdb │ │ │ ├── forx.itp │ │ │ ├── forx.pdb │ │ │ ├── imia.itp │ │ │ ├── imia.pdb │ │ │ ├── iodb.itp │ │ │ ├── iodb.pdb │ │ │ ├── mamm.itp │ │ │ ├── mamm.pdb │ │ │ ├── mamx.itp │ │ │ ├── mamx.pdb │ │ │ ├── mamy.itp │ │ │ ├── mamy.pdb │ │ │ ├── meoh.itp │ │ │ ├── meoh.pdb │ │ │ ├── meox.itp │ │ │ ├── meox.pdb │ │ │ ├── mqtr │ │ │ │ ├── benz.mqtr │ │ │ │ ├── chlb.mqtr │ │ │ │ └── tolu.mqtr │ │ │ ├── phen.itp │ │ │ ├── phen.pdb │ │ │ ├── prox.itp │ │ │ ├── prox.pdb │ │ │ ├── prpa.itp │ │ │ ├── prpa.pdb │ │ │ ├── prpx.itp │ │ │ ├── prpx.pdb │ │ │ ├── pyr1.itp │ │ │ ├── pyr1.pdb │ │ │ ├── sol.pdb │ │ │ ├── tolu.itp │ │ │ └── tolu.pdb │ │ ├── nbfix.itp │ │ ├── silcs.itp │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ ├── tip4p.itp │ │ └── watermodels.dat │ └── quinoline │ │ ├── LIG_ffbonded.itp │ │ ├── after_cg.g96 │ │ ├── cg.tpr │ │ ├── conf.gro │ │ ├── eigenfreq.xvg │ │ ├── eigenval.xvg │ │ ├── eigenvec.trr │ │ ├── ener.edr │ │ ├── md.log │ │ ├── mdout.mdp │ │ ├── minimize.log │ │ ├── minimize.tpr │ │ ├── nm.log │ │ ├── nm.mtx │ │ ├── nm.tpr │ │ ├── old.top │ │ ├── quinoline-g4.log.gz │ │ ├── spectrum.xvg │ │ ├── topol.top │ │ └── traj.trr ├── GAFF-ESP │ ├── N-methylacetamide │ │ ├── N-methylacetamide-3-oep.log.gz │ │ ├── after_cg.g96 │ │ ├── conf.gro │ │ ├── eigenfreq.xvg │ │ ├── eigenval.xvg │ │ ├── eigenvec.trr │ │ ├── ener.edr │ │ ├── mdout.mdp │ │ ├── minimize.log │ │ ├── minimize.tpr │ │ ├── nm.log │ │ ├── nm.mtx │ │ ├── nm.tpr │ │ ├── old.top │ │ ├── topol.top │ │ └── traj.trr │ ├── carbon-monoxide │ │ ├── after_cg.g96 │ │ ├── carbon-monoxide-3-oep.log.gz │ │ ├── carbon-monoxide-g4.log.gz │ │ ├── conf.gro │ │ ├── eigenfreq.xvg │ │ ├── eigenval.xvg │ │ ├── eigenvec.trr │ │ ├── ener.edr │ │ ├── mdout.mdp │ │ ├── minimize.log │ │ ├── minimize.tpr │ │ ├── nm.log │ │ ├── nm.mtx │ │ ├── nm.tpr │ │ ├── old.top │ │ ├── spectrum.xvg │ │ ├── topol.top │ │ └── traj.trr │ └── quinoline │ │ ├── after_cg.g96 │ │ ├── conf.gro │ │ ├── eigenfreq.xvg │ │ ├── eigenval.xvg │ │ ├── eigenvec.trr │ │ ├── ener.edr │ │ ├── mdout.mdp │ │ ├── minimize.log │ │ ├── minimize.tpr │ │ ├── nm.log │ │ ├── nm.mtx │ │ ├── nm.tpr │ │ ├── old.top │ │ ├── quinoline-g4.log.gz │ │ ├── spectrum.xvg │ │ ├── topol.top │ │ └── traj.trr └── MDP │ ├── cg.mdp │ └── nm.mdp ├── refs └── alfred_refs.bib └── scripts ├── CalculateSpectrum ├── mk_spectrum.py ├── spectrum_classes.py └── spectrum_functions.py ├── GenerateSpectra ├── get_exp_data.py ├── get_exp_data.sh ├── mixing_spectra.py ├── mk_spectra.py ├── run_spectrum.sh ├── spectrum_classes.py ├── spectrum_functions.py └── spectrum_functions.pyc ├── calculate_intensity_from_charge_theory_and_example.ipynb ├── charge_instead_of_dipole_moment.ipynb ├── mk_spectrum.py ├── remove_nan.py ├── run_nm.py └── visualization_of_spectra.ipynb /README.md: -------------------------------------------------------------------------------- 1 | # IR-Spectra 2 | Code and examples to compute IR spectra from normal mode analysis 3 | 4 | IR spectra can be computed based on normal mode analysis from either quantum chemistry or force fields. In this repository we gather information and scripts to compute spectra in the context of the GROMACS (http://www.gromacs.org) simulation software. 5 | 6 | Force field calculations of frequency-dependent properties have been published here: https://pubs.acs.org/doi/10.1021/acs.jpca.8b09867 and eventually the resulting spectra will be published on http://virtualchemistry.org. 7 | 8 | We have published two papers related to this work: 9 | + Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields 10 | Henning Henschel, Alfred T. Andersson, Willem Jespers, Mohammad Mehdi Ghahremanpour, and David van der Spoel, https://doi.org/10.1021/acs.jctc.0c00126 11 | + An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra 12 | Henning Henschel and David van der Spoel, https://doi.org/10.1021/acs.jpclett.0c01655 13 | 14 | Note for using the scripts: 15 | =========================== 16 | 17 | GROMACS should be compiled in double precision using: 18 | 19 | cmake -DGMX_DOUBLE=ON 20 | 21 | Important literature 22 | ==================== 23 | 24 | https://pubs.acs.org/doi/10.1021/acs.chemrev.9b00007 Review focusing on high-accuracy computational spectroscopy. 25 | 26 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877123/ About the NIST Quantitative Infrared Database. 27 | 28 | https://link.springer.com/article/10.1007/s00249-014-1005-6 Calculation of the infrared spectra of proteins. 29 | 30 | https://link.springer.com/article/10.1007/s00249-013-0927-8 Fast calculation of the infrared spectra of large biomolecules. 31 | 32 | Other related projects 33 | ====================== 34 | 35 | The Virtual Multifrequency Spectrometer project http://dreamslab.sns.it/vms/index.php 36 | -------------------------------------------------------------------------------- /docs/python-libs.tex: -------------------------------------------------------------------------------- 1 | These are some Python libs developed by other groups: 2 | 3 | 1- https://github.com/charlesll/rampy 4 | 2- https://pypi.org/project/pyvib2/ 5 | -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/LIG_ffbonded.itp: -------------------------------------------------------------------------------- 1 | ; This force field generated by mol2tortp for ligand specific params 2 | ; Copyright University of Maryland, School of Pharmacy 3 | 4 | -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/after_cg.g96: -------------------------------------------------------------------------------- 1 | TITLE 2 | Ligand 3 | END 4 | POSITION 5 | 1 LIG C1 1 2.172300998 1.924987134 1.988316348 6 | 1 LIG H2 2 2.267481713 1.973723293 1.957838064 7 | 1 LIG H3 3 2.151608275 1.840572935 1.919253605 8 | 1 LIG H4 4 1.840000654 2.153883666 2.083242082 9 | 1 LIG C5 5 2.062638015 2.024319497 1.982036934 10 | 1 LIG O6 6 2.083984382 2.139634661 1.947410322 11 | 1 LIG N7 7 1.940685101 1.980653945 2.016088855 12 | 1 LIG H8 8 1.808452452 2.108209343 1.911687733 13 | 1 LIG C9 9 1.825413440 2.067738732 2.014101592 14 | 1 LIG H10 10 1.734044641 2.012688407 2.045560476 15 | 1 LIG H11 11 1.928039954 1.886060305 2.043598519 16 | 1 LIG H12 12 2.183350375 1.886528082 2.091865471 17 | END 18 | BOX 19 | 4.000000000 4.000000000 4.000000000 20 | END 21 | -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/conf.gro: -------------------------------------------------------------------------------- 1 | GRoups of Organic Molecules in ACtion for Science 2 | 12 3 | 1LIG C1 1 2.174 1.923 1.993 4 | 1LIG H2 2 2.243 1.958 1.916 5 | 1LIG H3 3 2.136 1.824 1.965 6 | 1LIG H4 4 1.856 2.167 2.032 7 | 1LIG C5 5 2.065 2.027 2.011 8 | 1LIG O6 6 2.091 2.142 2.043 9 | 1LIG N7 7 1.938 1.983 1.991 10 | 1LIG H8 8 1.766 2.075 1.911 11 | 1LIG C9 9 1.821 2.068 2.005 12 | 1LIG H10 10 1.754 2.031 2.082 13 | 1LIG H11 11 1.924 1.887 1.966 14 | 1LIG H12 12 2.230 1.914 2.086 15 | 4.00000 4.00000 4.00000 16 | -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/eigenfreq.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Oct 7 19:25:41 2018 2 | # Created by: 3 | # :-) GROMACS - gmx nmeig, 2019-dev-20181004-83c2c3a2f (double precision) (-: 4 | # 5 | # Executable: /Users/spoel/software-master/bin/gmx_mpi_d 6 | # Data prefix: /Users/spoel/software-master 7 | # Working dir: /Users/spoel/Liquids/FORCE_FIELD/THERMO/CGenFF/N-methylacetamide 8 | # Command line: 9 | # gmx_mpi_d nmeig -maxspec 5000 -s nm -f nm.mtx -sigma 1 -last 500 -scale 1.035000 10 | # gmx nmeig is part of G R O M A C S: 11 | # 12 | # Grunge ROck MAChoS 13 | # 14 | @ title "Eigenfrequencies" 15 | @ xaxis label "Eigenvector index" 16 | @ yaxis label "Wavenumber [cm\S-1\N]" 17 | @TYPE xy 18 | @ subtitle "mass weighted" 19 | 1 0 20 | 2 0 21 | 3 0 22 | 4 0 23 | 5 0.00394591 24 | 6 0.0281569 25 | 7 65.066 26 | 8 94.7582 27 | 9 183.608 28 | 10 272.664 29 | 11 432.44 30 | 12 573.845 31 | 13 580.492 32 | 14 717.809 33 | 15 776.635 34 | 16 949.454 35 | 17 996.381 36 | 18 1056.24 37 | 19 1081.07 38 | 20 1088.18 39 | 21 1267.3 40 | 22 1384.43 41 | 23 1412.51 42 | 24 1415.79 43 | 25 1418.63 44 | 26 1426.94 45 | 27 1481.39 46 | 28 1588.18 47 | 29 1682.6 48 | 30 2852.81 49 | 31 2914.01 50 | 32 2914.72 51 | 33 2917.04 52 | 34 2975.21 53 | 35 2975.37 54 | 36 3325.5 55 | -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/eigenval.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Oct 7 19:25:41 2018 2 | # Created by: 3 | # :-) GROMACS - gmx nmeig, 2019-dev-20181004-83c2c3a2f (double precision) (-: 4 | # 5 | # Executable: /Users/spoel/software-master/bin/gmx_mpi_d 6 | # Data prefix: /Users/spoel/software-master 7 | # Working dir: /Users/spoel/Liquids/FORCE_FIELD/THERMO/CGenFF/N-methylacetamide 8 | # Command line: 9 | # gmx_mpi_d nmeig -maxspec 5000 -s nm -f nm.mtx -sigma 1 -last 500 -scale 1.035000 10 | # gmx nmeig is part of G R O M A C S: 11 | # 12 | # Great Red Oystrich Makes All Chemists Sane 13 | # 14 | @ title "Eigenvalues" 15 | @ xaxis label "Eigenvalue index" 16 | @ yaxis label "Eigenvalue [Gromacs units]" 17 | @TYPE xy 18 | @ subtitle "mass weighted" 19 | 1 -0.000456702 20 | 2 -6.15176e-05 21 | 3 -3.60131e-07 22 | 4 -5.55521e-08 23 | 5 5.52453e-07 24 | 6 2.813e-05 25 | 7 150.213 26 | 8 318.592 27 | 9 1196.14 28 | 10 2637.9 29 | 11 6635.19 30 | 12 11684 31 | 13 11956.2 32 | 14 18281.8 33 | 15 21401 34 | 16 31985.2 35 | 17 35225.1 36 | 18 39584.5 37 | 19 41467.9 38 | 20 42014.6 39 | 21 56985.4 40 | 22 68005.3 41 | 23 70792.3 42 | 24 71121 43 | 25 71407 44 | 26 72245.6 45 | 27 77864.9 46 | 28 89495.4 47 | 29 100453 48 | 30 288766 49 | 31 301288 50 | 32 301436 51 | 33 301916 52 | 34 314076 53 | 35 314110 54 | 36 392387 55 | -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/eigenvec.trr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/CGenFF/N-methylacetamide/eigenvec.trr -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/ener.edr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/CGenFF/N-methylacetamide/ener.edr -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/minimize.tpr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/CGenFF/N-methylacetamide/minimize.tpr -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/nm.mtx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/CGenFF/N-methylacetamide/nm.mtx -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/nm.tpr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/CGenFF/N-methylacetamide/nm.tpr -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/old.top: -------------------------------------------------------------------------------- 1 | ; Topology generated using molcal v1.0 2 | ; For use with CGenFF force-field version 4.1 3 | ; 4 | ; Include forcefield parameters 5 | #include "./charmm36.ff/forcefield.itp" 6 | ; 7 | ; Include ligand specific parameters 8 | # include "./LIG_ffbonded.itp" 9 | ; 10 | [ moleculetype ] 11 | ; Name nrexcl 12 | Other 3 13 | ; 14 | [ atoms ] 15 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 16 | ; residue 1 LIG rtp LIG q +0.0 17 | 1 CG331 1 LIG C1 1 -0.267 12.011 ; qtot -0.267 18 | 2 HGA3 1 LIG H2 2 0.09 1.008 ; qtot 0.09 19 | 3 HGA3 1 LIG H3 3 0.09 1.008 ; qtot 0.09 20 | 4 HGA3 1 LIG H4 4 0.09 1.008 ; qtot 0.09 21 | 5 CG2O1 1 LIG C5 5 0.516 12.011 ; qtot 0.516 22 | 6 OG2D1 1 LIG O6 6 -0.517 15.9994 ; qtot -0.517 23 | 7 NG2S1 1 LIG N7 7 -0.475 14.007 ; qtot -0.475 24 | 8 HGA3 1 LIG H8 8 0.09 1.008 ; qtot 0.09 25 | 9 CG331 1 LIG C9 9 -0.105 12.011 ; qtot -0.105 26 | 10 HGA3 1 LIG H10 10 0.09 1.008 ; qtot 0.09 27 | 11 HGP1 1 LIG H11 11 0.308 1.008 ; qtot 0.308 28 | 12 HGA3 1 LIG H12 12 0.09 1.008 ; qtot 0.09 29 | 30 | [ bonds ] 31 | ; ai aj funct c0 c1 c2 c3 32 | 8 9 1 33 | 2 1 1 34 | 3 1 1 35 | 11 7 1 36 | 7 9 1 37 | 7 5 1 38 | 1 5 1 39 | 1 12 1 40 | 9 4 1 41 | 9 10 1 42 | 5 6 1 43 | 44 | [ pairs ] 45 | ; ai aj funct c0 c1 c2 c3 46 | 1 9 1 47 | 1 11 1 48 | 2 6 1 49 | 2 7 1 50 | 3 6 1 51 | 3 7 1 52 | 4 5 1 53 | 4 11 1 54 | 5 8 1 55 | 5 10 1 56 | 6 9 1 57 | 6 11 1 58 | 6 12 1 59 | 7 12 1 60 | 8 11 1 61 | 10 11 1 62 | 63 | [ angles ] 64 | ; ai aj ak funct c0 c1 c2 c3 65 | 2 1 3 5 66 | 2 1 5 5 67 | 2 1 12 5 68 | 3 1 5 5 69 | 3 1 12 5 70 | 5 1 12 5 71 | 7 5 1 5 72 | 7 5 6 5 73 | 1 5 6 5 74 | 11 7 9 5 75 | 11 7 5 5 76 | 9 7 5 5 77 | 8 9 7 5 78 | 8 9 4 5 79 | 8 9 10 5 80 | 7 9 4 5 81 | 7 9 10 5 82 | 4 9 10 5 83 | 84 | [ dihedrals ] 85 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 86 | 11 7 9 8 9 87 | 11 7 9 4 9 88 | 11 7 9 10 9 89 | 5 7 9 8 9 90 | 5 7 9 4 9 91 | 5 7 9 10 9 92 | 11 7 5 1 9 93 | 11 7 5 6 9 94 | 9 7 5 1 9 95 | 9 7 5 6 9 96 | 2 1 5 7 9 97 | 2 1 5 6 9 98 | 3 1 5 7 9 99 | 3 1 5 6 9 100 | 12 1 5 7 9 101 | 12 1 5 6 9 102 | 103 | [ dihedrals ] 104 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 105 | 5 1 7 6 2 106 | 107 | 108 | 109 | ; Include Position restraint file 110 | #ifdef POSRES 111 | #include "posre.itp" 112 | #endif 113 | 114 | ; Include water topology 115 | #include "./charmm36.ff/tip3p.itp" 116 | 117 | #ifdef POSRES_WATER 118 | ; Position restraint for each water oxygen 119 | [ position_restraints ] 120 | ; i funct fcx fcy fcz 121 | 1 1 1000 1000 1000 122 | #endif 123 | 124 | ; Include topology for ions 125 | #include "./charmm36.ff/ions.itp" 126 | 127 | [ system ] 128 | ; Name 129 | Ligand 130 | 131 | [ molecules ] 132 | ; Compound #mols 133 | Other 1 134 | -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/output: -------------------------------------------------------------------------------- 1 | Using begin = 1 and end = 36 2 | Full matrix storage format, nrow=36, ncols=36 3 | Writing eigenfrequencies - negative eigenvalues will be set to zero. 4 | Translational entropy 162.381 J/mol K 5 | Rotational entropy 106.302 J/mol K 6 | Vibrational entropy 59.084 J/mol K 7 | Total entropy 327.767 J/mol K 8 | Heat capacity 85.9483 J/mol K 9 | Internal energy 281.746 kJ/mol 10 | Zero-point energy 265.092 kJ/mol 11 | -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/topol.top: -------------------------------------------------------------------------------- 1 | ; Topology generated using molcal v1.0 2 | ; For use with CGenFF force-field version 4.1 3 | ; 4 | ; Include forcefield parameters 5 | #include "forcefield.itp" 6 | 7 | ; 8 | ; Include ligand specific parameters 9 | # include "./LIG_ffbonded.itp" 10 | ; 11 | [ moleculetype ] 12 | ; Name nrexcl 13 | Other 3 14 | ; 15 | [ atoms ] 16 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 17 | ; residue 1 LIG rtp LIG q +0.0 18 | 1 CG331 1 LIG C1 1 -0.267 12.011 ; qtot -0.267 19 | 2 HGA3 1 LIG H2 2 0.09 1.008 ; qtot 0.09 20 | 3 HGA3 1 LIG H3 3 0.09 1.008 ; qtot 0.09 21 | 4 HGA3 1 LIG H4 4 0.09 1.008 ; qtot 0.09 22 | 5 CG2O1 1 LIG C5 5 0.516 12.011 ; qtot 0.516 23 | 6 OG2D1 1 LIG O6 6 -0.517 15.9994 ; qtot -0.517 24 | 7 NG2S1 1 LIG N7 7 -0.475 14.007 ; qtot -0.475 25 | 8 HGA3 1 LIG H8 8 0.09 1.008 ; qtot 0.09 26 | 9 CG331 1 LIG C9 9 -0.105 12.011 ; qtot -0.105 27 | 10 HGA3 1 LIG H10 10 0.09 1.008 ; qtot 0.09 28 | 11 HGP1 1 LIG H11 11 0.308 1.008 ; qtot 0.308 29 | 12 HGA3 1 LIG H12 12 0.09 1.008 ; qtot 0.09 30 | 31 | [ bonds ] 32 | ; ai aj funct c0 c1 c2 c3 33 | 8 9 1 34 | 2 1 1 35 | 3 1 1 36 | 11 7 1 37 | 7 9 1 38 | 7 5 1 39 | 1 5 1 40 | 1 12 1 41 | 9 4 1 42 | 9 10 1 43 | 5 6 1 44 | 45 | [ pairs ] 46 | ; ai aj funct c0 c1 c2 c3 47 | 1 9 1 48 | 1 11 1 49 | 2 6 1 50 | 2 7 1 51 | 3 6 1 52 | 3 7 1 53 | 4 5 1 54 | 4 11 1 55 | 5 8 1 56 | 5 10 1 57 | 6 9 1 58 | 6 11 1 59 | 6 12 1 60 | 7 12 1 61 | 8 11 1 62 | 10 11 1 63 | 64 | [ angles ] 65 | ; ai aj ak funct c0 c1 c2 c3 66 | 2 1 3 5 67 | 2 1 5 5 68 | 2 1 12 5 69 | 3 1 5 5 70 | 3 1 12 5 71 | 5 1 12 5 72 | 7 5 1 5 73 | 7 5 6 5 74 | 1 5 6 5 75 | 11 7 9 5 76 | 11 7 5 5 77 | 9 7 5 5 78 | 8 9 7 5 79 | 8 9 4 5 80 | 8 9 10 5 81 | 7 9 4 5 82 | 7 9 10 5 83 | 4 9 10 5 84 | 85 | [ dihedrals ] 86 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 87 | 11 7 9 8 9 88 | 11 7 9 4 9 89 | 11 7 9 10 9 90 | 5 7 9 8 9 91 | 5 7 9 4 9 92 | 5 7 9 10 9 93 | 11 7 5 1 9 94 | 11 7 5 6 9 95 | 9 7 5 1 9 96 | 9 7 5 6 9 97 | 2 1 5 7 9 98 | 2 1 5 6 9 99 | 3 1 5 7 9 100 | 3 1 5 6 9 101 | 12 1 5 7 9 102 | 12 1 5 6 9 103 | 104 | [ dihedrals ] 105 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 106 | 5 1 7 6 2 107 | 108 | 109 | 110 | ; Include Position restraint file 111 | #ifdef POSRES 112 | #include "posre.itp" 113 | #endif 114 | 115 | ; Include water topology 116 | #include "tip3p.itp" 117 | 118 | 119 | #ifdef POSRES_WATER 120 | ; Position restraint for each water oxygen 121 | [ position_restraints ] 122 | ; i funct fcx fcy fcz 123 | 1 1 1000 1000 1000 124 | #endif 125 | 126 | ; Include topology for ions 127 | #include "ions.itp" 128 | 129 | 130 | [ system ] 131 | ; Name 132 | Ligand 133 | 134 | [ molecules ] 135 | ; Compound #mols 136 | Other 1 137 | -------------------------------------------------------------------------------- /examples/CGenFF/N-methylacetamide/traj.trr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/CGenFF/N-methylacetamide/traj.trr -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/bugs: -------------------------------------------------------------------------------- 1 | Encountered a second block of parameters for dihedral type 9 for the same 2 | atoms, with either different parameters and/or the first block has 3 | multiple lines. This is not supported. 4 | 5 | 6 | 13-dimethyl-13-diazinan-2-one 7 | ERROR 1 [file LIG_ffbonded.itp, line 15]: 8 | ERROR 2 [file LIG_ffbonded.itp, line 18]: 9 | 10 | 4-methyl-5-thiazoleethanol 11 | ERROR 1 [file LIG_ffbonded.itp, line 14]: 12 | 13 | 14-dimethylcyclopent-1-ene 14 | ERROR 1 [file LIG_ffbonded.itp, line 10]: 15 | 16 | 1-methyl-4--propan-2-yl-cyclopent-1-ene 17 | ERROR 1 [file LIG_ffbonded.itp, line 14]: 18 | 19 | arginine 20 | ERROR 1 [file LIG_ffbonded.itp, line 10]: 21 | ERROR 2 [file LIG_ffbonded.itp, line 12]: 22 | 23 | valine 24 | ERROR 1 [file LIG_ffbonded.itp, line 6]: 25 | 26 | glutamic-acid 27 | ERROR 1 [file LIG_ffbonded.itp, line 7]: 28 | 29 | 4-ethylcyclopent-1-ene 30 | ERROR 1 [file LIG_ffbonded.itp, line 18]: 31 | 32 | 3-methyl-1--propan-2-yl-cyclopent-1-ene 33 | ERROR 1 [file LIG_ffbonded.itp, line 24]: 34 | ERROR 2 [file LIG_ffbonded.itp, line 34]: 35 | 36 | benzeneacetonitrile 37 | ERROR 1 [file LIG_ffbonded.itp, line 6]: 38 | 39 | 1-butylcyclopent-1-ene 40 | ERROR 1 [file LIG_ffbonded.itp, line 15]: 41 | 42 | 123-trimethylcyclopent-1-ene 43 | ERROR 1 [file LIG_ffbonded.itp, line 16]: 44 | ERROR 2 [file LIG_ffbonded.itp, line 22]: 45 | 46 | 13-dimethylcyclopent-1-ene 47 | ERROR 1 [file LIG_ffbonded.itp, line 13]: 48 | ERROR 2 [file LIG_ffbonded.itp, line 21]: 49 | 50 | hexamethyleneimine 51 | ERROR 1 [file LIG_ffbonded.itp, line 9]: 52 | 53 | 3-methylcyclopentene 54 | ERROR 1 [file LIG_ffbonded.itp, line 11]: 55 | ERROR 2 [file LIG_ffbonded.itp, line 13]: 56 | 57 | 1-methylpyrazole 58 | ERROR 1 [file LIG_ffbonded.itp, line 6]: 59 | 60 | 1-methylpyrrole 61 | ERROR 1 [file LIG_ffbonded.itp, line 6]: 62 | 63 | piperidine-axial 64 | ERROR 1 [file LIG_ffbonded.itp, line 9]: 65 | 66 | 2-propylbenzothiophene 67 | ERROR 1 [file LIG_ffbonded.itp, line 11] 68 | 69 | N-prop-2-enylprop-2-en-1-amine 70 | ERROR 1 [file LIG_ffbonded.itp, line 6]: 71 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/forcefield.itp: -------------------------------------------------------------------------------- 1 | ; This force field generated by charmm2gmx.py from 2 | ; multiple charmm parameter files 3 | ; and multiple charmm topology files 4 | #define _FF_CHARMM 5 | 6 | ; This GROMACS version was created from: 7 | ; CHARMM parameters: multiple files 8 | ; CHARMM topology: multiple files 9 | ; Please see forcefield.doc for files and references 10 | [ defaults ] 11 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 12 | 1 2 yes 1.0 1.0 13 | 14 | #include "ffnonbonded.itp" 15 | #include "ffbonded.itp" 16 | #include "hack.itp" 17 | #include "gb.itp" 18 | 19 | ; Allow the user to specify CHARMM36 parameters, instead 20 | ; Default behavior is to use CHARMM36m 21 | #ifdef USE_OLD_C36 22 | #include "old_c36_cmap.itp" 23 | #else 24 | #include "cmap.itp" 25 | #endif 26 | 27 | #include "nbfix.itp" 28 | #include "silcs.itp" 29 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/gb.itp: -------------------------------------------------------------------------------- 1 | 2 | [ implicit_genborn_params ] 3 | 4 | ; Atom type sar st pi gbr hct 5 | NH1 0.155 1 1.028 0.17063 0.79 ; N 6 | N 0.155 1 1 0.155 0.79 ; Proline backbone N 7 | NP 0.155 1 1 0.155 0.79 ; Proline backbone N for Proline N-terminus 8 | H 0.1 1 1 0.115 0.85 ; H 9 | CT1 0.180 1 1.276 0.190 0.72 ; C 10 | HB1 0.1 1 1 0.125 0.85 ; H 11 | CT3 0.200 1 0.880 0.190 0.72 ; C 12 | HA 0.1 1 1 0.125 0.85 ; H 13 | C 0.172 1 1.554 0.1875 0.72 ; C 14 | O 0.150 1 0.926 0.148 0.85 ; O 15 | CT2 0.190 1 1.045 0.190 0.72 ; C 16 | NC2 0.160 1 1.215 0.17063 0.79 ; N 17 | HC 0.1 1 1 0.115 0.85 ; H 18 | CC 0.172 1 1.554 0.1875 0.72 ; C 19 | CD 0.172 1 1.554 0.1875 0.72 ; carbonyl C (in COOH termini) 20 | NH2 0.160 1 1.215 0.17063 0.79 ; N 21 | OC 0.170 1 0.922 0.148 0.85 ; O 22 | OB 0.170 1 0.922 0.148 0.85 ; carbonyl O (in COOH termini) 23 | S 0.180 1 1.121 0.1775 0.96 ; S 24 | SM 0.180 1 1.121 0.1775 0.96 ; disulfide sulfur 25 | HS 0.1 1 1 0.125 0.85 ; H 26 | NR1 0.155 1 1.028 0.17063 0.79 ; N 27 | CPH1 0.172 1 1.554 0.1875 0.72 ; C 28 | CPH2 0.180 1 1.073 0.1875 0.72 ; C 29 | HR1 0.1 1 1 0.125 0.85 ; H 30 | HR2 0.1 1 1 0.125 0.85 ; H 31 | NR2 0.155 1 1.215 0.17063 0.79 ; N 32 | HR3 0.1 1 1 0.115 0.85 ; H 33 | NR3 0.155 1 1.215 0.17063 0.79 ; N 34 | NH3 0.160 1 1.215 0.1625 0.79 ; N 35 | HP 0.1 1 1 0.125 0.85 ; H 36 | CP3 0.190 1 1.045 0.190 0.72 ; C 37 | CP1 0.180 1 1.276 0.190 0.72 ; C 38 | CP2 0.190 1 1.045 0.190 0.72 ; C 39 | OH1 0.152 1 1.080 0.1535 0.85 ; O 40 | CY 0.172 0.012 1.554 0.1875 0.72 ; C 41 | CA 0.180 1 1.073 0.1875 0.72 ; C 42 | HP 0.1 1 1 0.125 0.85 ; H 43 | NY 0.155 1 1.028 0.17063 0.79 ; N 44 | CPT 0.172 0.012 1.554 0.1875 0.72 ; C 45 | MNH3 0 0 0 0 0 ; vsite (rigid tetrahedrical NH3 group) 46 | MNH2 0 0 0 0 0 ; vsite 47 | MCH3 0 0 0 0 0 ; vsite (rigid CH3 group) 48 | MCH3S 0 0 0 0 0 ; vsite 49 | MW 0 0 0 0 0 ; vsite 50 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/hack.itp: -------------------------------------------------------------------------------- 1 | [ dihedraltypes ] 2 | CG1N1 CG1T1 CG1T2 HGPAM1 9 0 0 1 3 | HGPAM1 CG1T2 CG1T2 HGPAM1 9 0 0 1 4 | HGA3 CG331 CG1T1 CG1T2 9 0 0 1 5 | CG331 CG1T1 CG1T2 HGPAM1 9 0 0 1 6 | HGA3 CG331 CG1T1 CG1T1 9 0 0 1 7 | CG331 CG1T1 CG1T1 CG331 9 0 0 1 8 | HGA2 CG321 CG1T1 CG1T2 9 0 0 1 9 | CG331 CG321 CG1T1 CG1T2 9 0 0 1 10 | CG321 CG1T1 CG1T2 HGPAM1 9 0 0 1 11 | CG1T2 CG1T1 CG1T1 CG1T1 9 0 0 1 12 | CG1T1 CG1T1 CG1T1 CG1T1 9 0 0 1 13 | CG1T1 CG1T1 CG1T2 HGPAM1 9 0 0 1 14 | CG321 CG1T1 CG1T1 CG321 9 0 0 1 15 | CG1T1 CG1T1 CG321 HGA2 9 0 0 1 16 | CG1T1 CG1T1 CG321 CG321 9 0 0 1 17 | NG1T1 CG1N1 CG321 CG1N1 9 0 0 1 18 | NG1T1 CG1N1 CG321 HGA2 9 0 0 1 19 | FGA1 CG1T1 CG1T1 BRGA1 9 0 0 1 20 | HGPAM1 CG1T2 CG1T1 CG2D1 9 0 0 1 21 | CG1T2 CG1T1 CG2D1 CG2D2 9 0 0 1 22 | CG1T2 CG1T1 CG2D1 HGA4 9 0 0 1 23 | NG1T1 CG1N1 CG2D1 CG2D1 9 0 0 1 24 | NG1T1 CG1N1 CG2D1 HGA4 9 0 0 1 25 | CG331 CG2O5 CG1T1 CG1T2 9 0 0 1 26 | OG2D3 CG2O5 CG1T1 CG1T2 9 0 0 1 27 | CG2O5 CG1T1 CG1T2 HGPAM1 9 0 0 1 28 | CG331 CG321 CG1T1 CG1T1 9 0 0 1 29 | CG331 CG321 CG1T1 CG1T1 9 0 0 1 30 | CG1T2 CG1T1 CG1T1 CG1T2 9 0 0 1 31 | NG1T1 CG1N1 CG321 CG321 9 0 0 1 32 | OG2N1 NG2O1 CG1T1 CG1T2 9 0 0 1 33 | NG2O1 CG1T1 CG1T2 HGPAM1 9 0 0 1 34 | CG1T1 CG1T1 CG1T1 CG331 9 0 0 1 35 | HGPAM1 CG1T2 CG1T1 CG311 9 0 0 1 36 | CG1T2 CG1T1 CG311 CG331 9 0 0 1 37 | CG1T2 CG1T1 CG311 CG321 9 0 0 1 38 | CG1T2 CG1T1 CG311 HGA1 9 0 0 1 39 | CG1T2 CG1T1 CG321 CG311 9 0 0 1 40 | FGA3 CG302 CG1T1 CG1T2 9 0 0 1 41 | CG302 CG1T1 CG1T2 HGPAM1 9 0 0 1 42 | HGPAM1 CG1T2 CG1T1 BRGA1 9 0 0 1 43 | HGPAM1 CG1T2 CG1T1 CLGA1 9 0 0 1 44 | HGPAM1 CG1T2 CG1T1 IGR1 9 0 0 1 45 | CG331 CG1T1 CG1T1 CG321 9 0 0 1 46 | NG1T1 CG1N1 CG321 CG2O2 9 0 0 1 47 | CG331 CG1T1 CG1T1 CG311 9 0 0 1 48 | CG1T1 CG1T1 CG311 CG321 9 0 0 1 49 | CG1T1 CG1T1 CG311 CG331 9 0 0 1 50 | CG1T1 CG1T1 CG311 HGA1 9 0 0 1 51 | CG321 CG321 CG1T1 CG1T2 9 0 0 1 52 | CG321 CG321 CG1T1 CG1T2 9 0 0 1 53 | NG1T1 CG1N1 CG2R61 CG2R61 9 0 0 1 54 | HGPAM1 CG1T2 CG1T1 FGA1 9 0 0 1 55 | HGR52 CG2O4 CG1T1 CG1T2 9 0 0 1 56 | OG2D1 CG2O4 CG1T1 CG1T2 9 0 0 1 57 | CG2O4 CG1T1 CG1T2 HGPAM1 9 0 0 1 58 | CG311 CG311 CG1T1 CG1T2 9 0 0 1 59 | CG331 CG1T1 CG1T1 NG321 9 0 0 1 60 | CG1T1 CG1T1 NG321 HGPAM2 9 0 0 1 61 | CG1T1 CG1T1 CG321 CG311 9 0 0 1 62 | CG331 OG301 CG1T1 CG1T2 9 0 0 1 63 | OG301 CG1T1 CG1T2 HGPAM1 9 0 0 1 64 | HGPAM1 CG1T2 CG1T1 CG322 9 0 0 1 65 | CG1T2 CG1T1 CG322 FGA1 9 0 0 1 66 | CG1T2 CG1T1 CG322 HGA6 9 0 0 1 67 | CG311 CG1T1 CG1T1 CG321 9 0 0 1 68 | NG1T1 CG1N1 CG321 CG2D1 9 0 0 1 69 | CG331 CG301 CG1T1 CG1T1 9 0 0 1 70 | CG301 CG1T1 CG1T1 CG331 9 0 0 1 71 | NG1T1 CG1N1 CG3C41 CG3C41 9 0 0 1 72 | NG1T1 CG1N1 CG3C41 HGA1 9 0 0 1 73 | NG1T1 CG1N1 CG321 CG311 9 0 0 1 74 | OG311 CG1T1 CG1T1 CG331 9 0 0 1 75 | CG1T1 CG1T1 OG311 HGP1 9 0 0 1 76 | NG1T1 CG1N1 SG311 CG1N1 9 0 0 1 77 | CG301 CG321 CG1T1 CG1T2 9 0 0 1 78 | CG2D2 CG2D1 CG1T1 CG1T1 9 0 0 1 79 | HGA4 CG2D1 CG1T1 CG1T1 9 0 0 1 80 | CG2D1 CG1T1 CG1T1 CG331 9 0 0 1 81 | NG1T1 CG1N1 CG301 CLGA3 9 0 0 1 82 | HGPAM1 CG1T2 CG1T1 CG2O2 9 0 0 1 83 | CG1T2 CG1T1 CG2O2 OG2D1 9 0 0 1 84 | CG1T2 CG1T1 CG2O2 OG302 9 0 0 1 85 | CLGA1 CG321 CG1T1 CG1T2 9 0 0 1 86 | CG1T2 CG1T1 CG321 NG321 9 0 0 1 87 | NG1T1 CG1N1 NG301 CG311 9 0 0 1 88 | CG1T2 CG1T1 CG321 OG311 9 0 0 1 89 | CG2D1 CG321 CG1T1 CG1T2 9 0 0 1 90 | NG1T1 CG1N1 NG321 HGPAM2 9 0 0 1 91 | HGPAM1 CG1T2 CG1T1 CG301 9 0 0 1 92 | CG331 CG301 CG1T1 CG1T2 9 0 0 1 93 | CG321 CG301 CG1T1 CG1T2 9 0 0 1 94 | CG2R61 CG2R61 CG1T1 CG1T2 9 0 0 1 95 | CG2R61 CG1T1 CG1T2 HGPAM1 9 0 0 1 96 | NG1T1 CG1N1 CG311 OG3C61 9 0 0 1 97 | NG1T1 CG1N1 CG311 CG321 9 0 0 1 98 | NG1T1 CG1N1 CG311 HGA1 9 0 0 1 99 | NG1T1 CG1N1 NG311 CG1N1 9 0 0 1 100 | NG1T1 CG1N1 NG311 HGPAM1 9 0 0 1 101 | NG1T1 CG1N1 CG321 CG331 9 0 0 1 102 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/ions.itp: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ moleculetype ] ; added by Bjelkmar Jan 2010, from c32b1/toppar/stream/toppar_water_ions.str 4 | ; molname nrexcl 5 | OH 1 6 | 7 | [ atoms ] 8 | ; id at type res nr residu name at name cg nr charge 9 | 1 OC 1 OH O1 1 -1.32 10 | 2 H 1 OH H1 1 0.32 11 | 12 | [ bonds ] 13 | ;i j funct length force.c. 14 | 1 2 1 0.09700 456056 ; hydroxyl bond 15 | 16 | [ moleculetype ] 17 | ; molname nrexcl 18 | LI 1 19 | 20 | [ atoms ] 21 | ; id at type res nr residu name at name cg nr charge 22 | 1 LIT 1 LI LI 1 1 23 | 24 | [ moleculetype ] 25 | ; molname nrexcl 26 | NA 1 27 | 28 | [ atoms ] 29 | ; id at type res nr residu name at name cg nr charge 30 | 1 SOD 1 NA NA 1 1 31 | 32 | [ moleculetype ] 33 | ; molname nrexcl 34 | K 1 35 | 36 | [ atoms ] 37 | ; id at type res nr residu name at name cg nr charge 38 | 1 POT 1 K K 1 1 39 | 40 | [ moleculetype ] 41 | ; molname nrexcl 42 | CS 1 43 | 44 | [ atoms ] 45 | ; id at type res nr residu name at name cg nr charge 46 | 1 CES 1 Ces Ces 1 1 47 | 48 | [ moleculetype ] 49 | ; molname nrexcl 50 | CL 1 51 | 52 | [ atoms ] 53 | ; id at type res nr residu name at name cg nr charge 54 | 1 CLA 1 CL CL 1 -1 55 | 56 | [ moleculetype ] 57 | ; molname nrexcl 58 | CA 1 59 | 60 | [ atoms ] 61 | ; id at type res nr residu name at name cg nr charge 62 | 1 CAL 1 Cal Cal 1 2 63 | 64 | [ moleculetype ] 65 | ; molname nrexcl 66 | MG 1 67 | 68 | [ atoms ] 69 | ; id at type res nr residu name at name cg nr charge 70 | #ifdef MG_ALLNER 71 | ; Use parameters from Allner et al. (DOI: 10.1021/ct3000734) 72 | 1 MGA 1 MG MG 1 2 73 | #else 74 | ; Standard CHARMM parameters 75 | 1 MG 1 MG MG 1 2 76 | #endif 77 | 78 | [ moleculetype ] 79 | ; molname nrexcl 80 | ZN 1 81 | 82 | [ atoms ] 83 | ; id at type res nr residu name at name cg nr charge 84 | 1 ZN 1 ZN ZN 1 2 85 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/merged.arn: -------------------------------------------------------------------------------- 1 | 2 | 3 | ; atom renaming specification 4 | ; residue gromacs forcefield 5 | * H HN 6 | 7 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/merged.c.tdb: -------------------------------------------------------------------------------- 1 | 2 | [ None ] 3 | 4 | ; CHARMM CTER 5 | [ COO- ] 6 | [ replace ] 7 | C C CC 12.011 0.34 8 | O OT1 OC 15.9994 -0.67 9 | OXT OT2 OC 15.9994 -0.67 10 | [ add ] 11 | 2 8 OT C CA N 12 | OC 15.9994 -0.67 -1 13 | [ impropers ] 14 | C CA OT2 OT1 15 | 16 | ; CHARMM CNEU 17 | [ COOH ] 18 | [ replace ] 19 | C C CD 12.011 0.72 20 | O OT1 OB 15.9994 -0.55 21 | OXT OT2 OH1 15.9994 -0.61 22 | [ add ] 23 | 2 8 OT C CA N 24 | OB 15.9994 -0.55 -1 25 | 1 2 HT2 OT2 C CA 26 | H 1.008 0.44 -1 27 | [ replace ] 28 | OT2 OT2 OH1 15.9994 -0.61 29 | [ impropers ] 30 | C CA OT2 OT1 31 | 32 | ; Created by Michel Cuendet. 33 | [ CT2 ] 34 | [ replace ] 35 | C CC 12.011 0.55 36 | O O 15.9994 -0.55 37 | [ add ] 38 | 1 2 NT C CA N 39 | NH2 14.0027 -0.62 -1 40 | 2 3 HT NT C CA 41 | H 1.008 0.00 -1 42 | [ replace ] 43 | HT1 H 1.008 0.30 ; this one is trans to O 44 | HT2 H 1.008 0.32 ; this one is cis to O 45 | [ impropers ] 46 | C NT CA O 47 | C CA NT O 48 | NT C HT1 HT2 49 | NT C HT2 HT1 50 | 51 | 52 | ; added by Justin Lemkul 53 | [ 3TER ] 54 | [ replace ] 55 | O3' ON5 15.9994 -0.66 56 | C3' CN7 12.011 0.14 57 | [ add ] 58 | 1 2 H3T O3' C3' C4' 59 | HN5 1.008 0.43 -1 60 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/merged.n.tdb: -------------------------------------------------------------------------------- 1 | 2 | [ None ] 3 | 4 | [ GLY-NH3+ ] 5 | [ replace ] 6 | N N NH3 14.0070 -0.30 7 | CA CA CT2 12.011 0.13 8 | [ Add ] 9 | 3 4 H N CA C 10 | HC 1.008 0.33 -1 11 | [ delete ] 12 | HN 13 | 14 | [ NH3+ ] 15 | [ replace ] 16 | N N NH3 14.0070 -0.30 17 | CA CA CT1 12.011 0.21 18 | HA HA HB1 1.008 0.10 19 | [ Add ] 20 | 3 4 H N CA C 21 | HC 1.008 0.33 -1 22 | [ delete ] 23 | HN 24 | 25 | [ PRO-NH2+ ] 26 | [ replace ] 27 | N N NP 14.0070 -0.07 28 | CA CA CP1 12.011 0.16 29 | CD CD CP3 12.011 0.16 30 | [ add ] 31 | 2 4 HN N CA C 32 | HC 1.008 0.24 -1 33 | 34 | ; Created by Michel Cuendet 35 | [ NH2 ] 36 | [ replace ] 37 | N NH2 14.007 -0.96 38 | CA CT1 12.011 0.19 39 | HA HB1 1.008 0.09 40 | [ add ] 41 | 2 4 H N CA C 42 | H 1.008 0.34 -1 43 | [ delete ] 44 | HN 45 | 46 | ; CHARMM NGNE patch, new 47 | [ GLY-NH2 ] 48 | [ replace ] 49 | N NH2 14.007 -0.96 50 | CA CT2 12.011 0.10 51 | HA1 HB2 1.008 0.09 52 | HA2 HB2 1.008 0.09 53 | [ add ] 54 | 2 4 H N CA C 55 | H 1.008 0.34 -1 56 | [ delete ] 57 | HN 58 | 59 | ; Created by Bjelkmar 60 | [ PRO-NH ] 61 | [ replace ] 62 | N NP 14.0070 -0.40 63 | CA CP1 12.011 -0.08 64 | CD CP3 12.011 -0.10 65 | [ add ] 66 | 1 4 H N CA C 67 | HC 1.008 0.31 -1 68 | 69 | ; added by Justin Lemkul 70 | [ 5TER ] 71 | [ replace ] 72 | O5' ON5 15.9994 -0.66 73 | C5' CN8B 12.011 0.05 74 | [ add ] 75 | 1 2 H5T O5' C5' C4' 76 | HN5 1.008 0.43 -1 77 | [ delete ] 78 | P 79 | O1P 80 | O2P 81 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/merged.r2b: -------------------------------------------------------------------------------- 1 | 2 | 3 | ; rtp residue to rtp building block table 4 | ;GMX Force-field 5 | HISD HSD 6 | HIS1 HSD 7 | HISE HSE 8 | HISH HSP 9 | LYSN LSN 10 | ASPH ASPP 11 | GLUH GLUP 12 | RA ADE 13 | RG GUA 14 | RU URA 15 | RC CYT 16 | 17 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/aald.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'aald.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Thu Apr 19 11:28:36 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f aald.pdb -p aald.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | AALD 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 AALD rtp AALD q 0.0 25 | 1 HGR52 1 AALD HA 1 0.09 1.008 ; qtot 0.09 26 | 2 CG2O4 1 AALD C 1 0.2 12.011 ; qtot 0.29 27 | 3 OG2D1 1 AALD O 1 -0.4 15.9994 ; qtot -0.11 28 | 4 CG331 1 AALD CB 1 -0.16 12.011 ; qtot -0.27 29 | 5 HGA3 1 AALD HB1 1 0.09 1.008 ; qtot -0.18 30 | 6 HGA3 1 AALD HB2 1 0.09 1.008 ; qtot -0.09 31 | 7 HGA3 1 AALD HB3 1 0.09 1.008 ; qtot 0 32 | 33 | [ bonds ] 34 | ; ai aj funct c0 c1 c2 c3 35 | 1 2 1 36 | 2 3 1 37 | 2 4 1 38 | 4 5 1 39 | 4 6 1 40 | 4 7 1 41 | 42 | [ pairs ] 43 | ; ai aj funct c0 c1 c2 c3 44 | 1 5 1 45 | 1 6 1 46 | 1 7 1 47 | 3 5 1 48 | 3 6 1 49 | 3 7 1 50 | 51 | [ angles ] 52 | ; ai aj ak funct c0 c1 c2 c3 53 | 1 2 3 5 54 | 1 2 4 5 55 | 3 2 4 5 56 | 2 4 5 5 57 | 2 4 6 5 58 | 2 4 7 5 59 | 5 4 6 5 60 | 5 4 7 5 61 | 6 4 7 5 62 | 63 | [ dihedrals ] 64 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 65 | 1 2 4 5 9 66 | 1 2 4 6 9 67 | 1 2 4 7 9 68 | 3 2 4 5 9 69 | 3 2 4 6 9 70 | 3 2 4 7 9 71 | 72 | [ dihedrals ] 73 | ; ai aj ak al funct c0 c1 c2 c3 74 | 1 3 4 2 2 75 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/aald.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 4/19/12 11:27:19 CREATED BY USER: prabhu 3 | ATOM 1 HA AALD 1 2.006 -1.020 -0.072 1.00 0.00 AALD 4 | ATOM 2 C AALD 1 1.514 -0.026 -0.023 1.00 0.00 AALD 5 | ATOM 3 O AALD 1 2.214 0.964 0.012 1.00 0.00 AALD 6 | ATOM 4 CB AALD 1 0.015 -0.015 -0.004 1.00 0.00 AALD 7 | ATOM 5 HB1 AALD 1 -0.346 1.035 0.046 1.00 0.00 AALD 8 | ATOM 6 HB2 AALD 1 -0.383 -0.487 -0.927 1.00 0.00 AALD 9 | ATOM 7 HB3 AALD 1 -0.362 -0.567 0.883 1.00 0.00 AALD 10 | TER 8 AALD 1 11 | END 12 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/acet.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'acet.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Tue Apr 17 16:07:46 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f acet.pdb -p acet.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | ACET 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 ACEY rtp ACEY q -1.0 25 | 1 CG331 1 ACET C1 1 -0.37 12.011 ; qtot -0.37 26 | 2 CG2O3 1 ACET C2 1 0.62 12.011 ; qtot 0.25 27 | 3 HGA3 1 ACET H1 1 0.09 1.008 ; qtot 0.34 28 | 4 HGA3 1 ACET H2 1 0.09 1.008 ; qtot 0.43 29 | 5 HGA3 1 ACET H3 1 0.09 1.008 ; qtot 0.52 30 | 6 OG2D2 1 ACET O1 1 -0.76 15.9994 ; qtot -0.24 31 | 7 OG2D2 1 ACET O2 1 -0.76 15.9994 ; qtot -1 32 | 33 | [ bonds ] 34 | ; ai aj funct c0 c1 c2 c3 35 | 1 2 1 36 | 1 3 1 37 | 1 4 1 38 | 1 5 1 39 | 2 6 1 40 | 2 7 1 41 | 42 | [ pairs ] 43 | ; ai aj funct c0 c1 c2 c3 44 | 3 6 1 45 | 3 7 1 46 | 4 6 1 47 | 4 7 1 48 | 5 6 1 49 | 5 7 1 50 | 51 | [ angles ] 52 | ; ai aj ak funct c0 c1 c2 c3 53 | 2 1 3 5 54 | 2 1 4 5 55 | 2 1 5 5 56 | 3 1 4 5 57 | 3 1 5 5 58 | 4 1 5 5 59 | 1 2 6 5 60 | 1 2 7 5 61 | 6 2 7 5 62 | 63 | [ dihedrals ] 64 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 65 | 3 1 2 6 9 66 | 3 1 2 7 9 67 | 4 1 2 6 9 68 | 4 1 2 7 9 69 | 5 1 2 6 9 70 | 5 1 2 7 9 71 | 72 | [ dihedrals ] 73 | ; ai aj ak al funct c0 c1 c2 c3 74 | 1 6 7 2 2 75 | 76 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/acet.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 4/17/12 15:27:58 CREATED BY USER: prabhu 3 | ATOM 1 C1 ACET 1 0.003 0.010 0.000 1.00 0.00 ACET 4 | ATOM 2 C2 ACET 1 1.510 0.004 -0.000 1.00 0.00 ACET 5 | ATOM 3 H1 ACET 1 -0.367 1.055 0.000 1.00 0.00 ACET 6 | ATOM 4 H2 ACET 1 -0.356 -0.516 0.906 1.00 0.00 ACET 7 | ATOM 5 H3 ACET 1 -0.356 -0.516 -0.906 1.00 0.00 ACET 8 | ATOM 6 O1 ACET 1 2.064 1.131 0.000 1.00 0.00 ACET 9 | ATOM 7 O2 ACET 1 2.041 -1.134 -0.000 1.00 0.00 ACET 10 | TER 8 ACET 1 11 | END 12 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/acey.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'acet.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Tue Apr 17 16:07:46 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f acet.pdb -p acet.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | ACEY 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 ACEY rtp ACEY q -1.0 25 | 1 CG331 1 ACEY C1 1 -0.37 12.011 ; qtot -0.37 26 | 2 CG2O3 1 ACEY C2 1 0.62 12.011 ; qtot 0.25 27 | 3 HGA3 1 ACEY H1 1 0.09 1.008 ; qtot 0.34 28 | 4 HGA3 1 ACEY H2 1 0.09 1.008 ; qtot 0.43 29 | 5 HGA3 1 ACEY H3 1 0.09 1.008 ; qtot 0.52 30 | 6 OG2D2 1 ACEY O1 1 -0.76 15.9994 ; qtot -0.24 31 | 7 OG2D2 1 ACEY O2 1 -0.76 15.9994 ; qtot -1 32 | 8 LQ 1 ACEY LPA 1 0.00 0.000 ; qtot -1 33 | 34 | [ bonds ] 35 | ; ai aj funct c0 c1 c2 c3 36 | 1 2 1 37 | 1 3 1 38 | 1 4 1 39 | 1 5 1 40 | 2 6 1 41 | 2 7 1 42 | 43 | [ pairs ] 44 | ; ai aj funct c0 c1 c2 c3 45 | 3 6 1 46 | 3 7 1 47 | 4 6 1 48 | 4 7 1 49 | 5 6 1 50 | 5 7 1 51 | 52 | [ angles ] 53 | ; ai aj ak funct c0 c1 c2 c3 54 | 2 1 3 5 55 | 2 1 4 5 56 | 2 1 5 5 57 | 3 1 4 5 58 | 3 1 5 5 59 | 4 1 5 5 60 | 1 2 6 5 61 | 1 2 7 5 62 | 6 2 7 5 63 | 64 | [ dihedrals ] 65 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 66 | 3 1 2 6 9 67 | 3 1 2 7 9 68 | 4 1 2 6 9 69 | 4 1 2 7 9 70 | 5 1 2 6 9 71 | 5 1 2 7 9 72 | 73 | [ dihedrals ] 74 | ; ai aj ak al funct c0 c1 c2 c3 75 | 1 6 7 2 2 76 | 77 | [ virtual_sites2 ] 78 | ; Vsite from funct a 79 | 8 1 2 1 0.5 80 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/acey.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 4/17/12 15:27:58 CREATED BY USER: prabhu 3 | ATOM 1 C1 ACEY 1 0.003 0.010 0.000 1.00 0.00 ACEY 4 | ATOM 2 C2 ACEY 1 1.510 0.004 -0.000 1.00 0.00 ACEY 5 | ATOM 3 H1 ACEY 1 -0.367 1.055 0.000 1.00 0.00 ACEY 6 | ATOM 4 H2 ACEY 1 -0.356 -0.516 0.906 1.00 0.00 ACEY 7 | ATOM 5 H3 ACEY 1 -0.356 -0.516 -0.906 1.00 0.00 ACEY 8 | ATOM 6 O1 ACEY 1 2.064 1.131 0.000 1.00 0.00 ACEY 9 | ATOM 7 O2 ACEY 1 2.041 -1.134 -0.000 1.00 0.00 ACEY 10 | ATOM 8 LPA ACEY 1 1.610 0.003 -0.000 1.00 0.00 ACEY 11 | TER 9 ACEY 1 12 | END 13 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/acox.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'aco.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Mon Feb 13 17:37:05 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f aco.pdb -p aco.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | ACOX 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 ACOXrtp ACOX q 0.0 25 | 1 OG2D3 1 ACOX O1 1 -0.48 15.9994 ; qtot -0.48 26 | 2 CG2O5 1 ACOX C1 1 0.4 12.011 ; qtot -0.08 27 | 3 CG331 1 ACOX C2 1 -0.23 12.011 ; qtot -0.31 28 | 4 CG331 1 ACOX C3 1 -0.23 12.011 ; qtot -0.54 29 | 5 HGA3 1 ACOX H21 1 0.09 1.008 ; qtot -0.45 30 | 6 HGA3 1 ACOX H22 1 0.09 1.008 ; qtot -0.36 31 | 7 HGA3 1 ACOX H23 1 0.09 1.008 ; qtot -0.27 32 | 8 HGA3 1 ACOX H31 1 0.09 1.008 ; qtot -0.18 33 | 9 HGA3 1 ACOX H32 1 0.09 1.008 ; qtot -0.09 34 | 10 HGA3 1 ACOX H33 1 0.09 1.008 ; qtot 0 35 | 11 LP 1 ACOX LPA 1 0.00 0.000 ; qtot 0 36 | 37 | [ bonds ] 38 | ; ai aj funct c0 c1 c2 c3 39 | 1 2 1 40 | 2 3 1 41 | 2 4 1 42 | 3 5 1 43 | 3 6 1 44 | 3 7 1 45 | 4 8 1 46 | 4 9 1 47 | 4 10 1 48 | 49 | [ pairs ] 50 | ; ai aj funct c0 c1 c2 c3 51 | 1 5 1 52 | 1 6 1 53 | 1 7 1 54 | 1 8 1 55 | 1 9 1 56 | 1 10 1 57 | 3 8 1 58 | 3 9 1 59 | 3 10 1 60 | 4 5 1 61 | 4 6 1 62 | 4 7 1 63 | 64 | [ angles ] 65 | ; ai aj ak funct c0 c1 c2 c3 66 | 1 2 3 5 67 | 1 2 4 5 68 | 3 2 4 5 69 | 2 3 5 5 70 | 2 3 6 5 71 | 2 3 7 5 72 | 5 3 6 5 73 | 5 3 7 5 74 | 6 3 7 5 75 | 2 4 8 5 76 | 2 4 9 5 77 | 2 4 10 5 78 | 8 4 9 5 79 | 8 4 10 5 80 | 9 4 10 5 81 | 82 | [ dihedrals ] 83 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 84 | 1 2 3 5 9 85 | 1 2 3 6 9 86 | 1 2 3 7 9 87 | 4 2 3 5 9 88 | 4 2 3 6 9 89 | 4 2 3 7 9 90 | 1 2 4 8 9 91 | 1 2 4 9 9 92 | 1 2 4 10 9 93 | 3 2 4 8 9 94 | 3 2 4 9 9 95 | 3 2 4 10 9 96 | 97 | [ dihedrals ] 98 | ; ai aj ak al funct c0 c1 c2 c3 99 | 1 4 3 2 2 100 | 101 | [ virtual_sites2 ] 102 | ; Vsite from funct a 103 | 11 1 2 1 0.99 104 | 105 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/acox.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 2/13/12 17:40:23 CREATED BY USER: prabhu 3 | ATOM 1 O1 ACOX 1 2.106 -0.855 0.676 1.00 0.00 ACOX 4 | ATOM 2 C1 ACOX 1 1.461 0.081 0.218 1.00 0.00 ACOX 5 | ATOM 3 C2 ACOX 1 0.014 -0.055 -0.116 1.00 0.00 ACOX 6 | ATOM 4 C3 ACOX 1 2.085 1.412 -0.034 1.00 0.00 ACOX 7 | ATOM 5 H21 ACOX 1 -0.314 -1.088 0.120 1.00 0.00 ACOX 8 | ATOM 6 H22 ACOX 1 -0.579 0.663 0.486 1.00 0.00 ACOX 9 | ATOM 7 H23 ACOX 1 -0.142 0.141 -1.196 1.00 0.00 ACOX 10 | ATOM 8 H31 ACOX 1 3.155 1.368 0.257 1.00 0.00 ACOX 11 | ATOM 9 H32 ACOX 1 2.009 1.665 -1.111 1.00 0.00 ACOX 12 | ATOM 10 H33 ACOX 1 1.573 2.187 0.571 1.00 0.00 ACOX 13 | ATOM 11 LPA ACOX 1 1.409 0.157 0.180 1.00 0.00 ACOX 14 | TER 12 ACOX 1 15 | END 16 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/anil.itp: -------------------------------------------------------------------------------- 1 | ; Created by atomgroup.write_gmx.itp() 2 | 3 | [ moleculetype ] 4 | ; Name nrexcl 5 | ANIL 3 6 | 7 | [ atoms ] 8 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 9 | ; residue 1 ANIL rtp ANIL q qsum 10 | 1 CG2R61 1 ANIL C1 1 -0.115 12.011 ; 11 | 2 HGR61 1 ANIL H2 2 0.115 1.008 ; 12 | 3 CG2R61 1 ANIL C3 3 -0.111 12.011 ; 13 | 4 HGR61 1 ANIL H4 4 0.115 1.008 ; 14 | 5 CG2R61 1 ANIL C5 5 -0.112 12.011 ; 15 | 6 HGR61 1 ANIL H6 6 0.115 1.008 ; 16 | 7 CG2R61 1 ANIL C7 7 0.058 12.011 ; 17 | 8 NG2S3 1 ANIL N8 8 -0.834 14.007 ; 18 | 9 CG2R61 1 ANIL C9 9 -0.112 12.011 ; 19 | 10 HGR61 1 ANIL H10 10 0.115 1.008 ; 20 | 11 CG2R61 1 ANIL C11 11 -0.111 12.011 ; 21 | 12 HGR61 1 ANIL H12 12 0.115 1.008 ; 22 | 13 HGP4 1 ANIL H1 13 0.381 1.008 ; 23 | 14 HGP4 1 ANIL H7 14 0.381 1.008 ; 24 | 25 | [ bonds ] 26 | ; ai aj funct c0 c1 c2 c3 27 | 1 2 1 28 | 1 11 1 29 | 1 3 1 30 | 3 4 1 31 | 3 5 1 32 | 5 6 1 33 | 5 7 1 34 | 7 9 1 35 | 7 8 1 36 | 8 13 1 37 | 8 14 1 38 | 9 10 1 39 | 9 11 1 40 | 11 12 1 41 | 42 | [ pairs ] 43 | ; ai aj funct c0 c1 c2 c3 44 | 1 10 1 45 | 1 6 1 46 | 1 7 1 47 | 2 9 1 48 | 2 4 1 49 | 2 12 1 50 | 2 5 1 51 | 3 9 1 52 | 3 12 1 53 | 3 8 1 54 | 4 11 1 55 | 4 6 1 56 | 4 7 1 57 | 5 11 1 58 | 5 13 1 59 | 5 14 1 60 | 5 10 1 61 | 6 9 1 62 | 6 8 1 63 | 7 12 1 64 | 8 10 1 65 | 8 11 1 66 | 9 13 1 67 | 9 14 1 68 | 10 12 1 69 | 70 | [ angles ] 71 | ; ai aj ak funct c0 c1 c2 c3 72 | 2 1 11 5 73 | 2 1 3 5 74 | 11 1 3 5 75 | 1 3 4 5 76 | 1 3 5 5 77 | 4 3 5 5 78 | 3 5 6 5 79 | 3 5 7 5 80 | 6 5 7 5 81 | 9 7 5 5 82 | 9 7 8 5 83 | 5 7 8 5 84 | 13 8 14 5 85 | 13 8 7 5 86 | 14 8 7 5 87 | 10 9 11 5 88 | 10 9 7 5 89 | 11 9 7 5 90 | 1 11 9 5 91 | 1 11 12 5 92 | 9 11 12 5 93 | 94 | [ dihedrals ] 95 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 96 | 2 1 11 9 9 97 | 2 1 11 12 9 98 | 3 1 11 9 9 99 | 3 1 11 12 9 100 | 2 1 3 4 9 101 | 2 1 3 5 9 102 | 11 1 3 4 9 103 | 11 1 3 5 9 104 | 1 3 5 6 9 105 | 1 3 5 7 9 106 | 4 3 5 6 9 107 | 4 3 5 7 9 108 | 3 5 7 9 9 109 | 3 5 7 8 9 110 | 6 5 7 9 9 111 | 6 5 7 8 9 112 | 5 7 9 10 9 113 | 5 7 9 11 9 114 | 8 7 9 10 9 115 | 8 7 9 11 9 116 | 9 7 8 13 9 117 | 9 7 8 14 9 118 | 5 7 8 13 9 119 | 5 7 8 14 9 120 | 10 9 11 1 9 121 | 10 9 11 12 9 122 | 7 9 11 1 9 123 | 7 9 11 12 9 124 | 125 | [ dihedrals ] 126 | ; ai aj ak al funct c0 c1 c2 c3 127 | 8 14 13 7 2 128 | 129 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/anil.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 9/10/12 11:43:31 CREATED BY USER: prabhu 3 | ATOM 1 C1 ANIL 1 -0.000 -0.000 0.000 1.00 0.00 ANIL 4 | ATOM 2 H2 ANIL 1 -0.540 -0.936 0.000 1.00 0.00 ANIL 5 | ATOM 3 C3 ANIL 1 1.401 -0.000 0.000 1.00 0.00 ANIL 6 | ATOM 4 H4 ANIL 1 1.942 -0.935 0.000 1.00 0.00 ANIL 7 | ATOM 5 C5 ANIL 1 2.101 1.216 -0.000 1.00 0.00 ANIL 8 | ATOM 6 H6 ANIL 1 3.181 1.209 -0.000 1.00 0.00 ANIL 9 | ATOM 7 C7 ANIL 1 1.404 2.430 -0.000 1.00 0.00 ANIL 10 | ATOM 8 N8 ANIL 1 2.097 3.631 -0.000 1.00 0.00 ANIL 11 | ATOM 9 C9 ANIL 1 0.003 2.428 -0.000 1.00 0.00 ANIL 12 | ATOM 10 H10 ANIL 1 -0.542 3.359 -0.000 1.00 0.00 ANIL 13 | ATOM 11 C11 ANIL 1 -0.700 1.214 0.000 1.00 0.00 ANIL 14 | ATOM 12 H12 ANIL 1 -1.780 1.216 0.000 1.00 0.00 ANIL 15 | ATOM 13 H1 ANIL 1 1.547 4.464 0.000 1.00 0.00 ANIL 16 | ATOM 14 H7 ANIL 1 3.094 3.570 0.000 1.00 0.00 ANIL 17 | TER 15 ANIL 1 18 | END 19 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/benx.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'system.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Thu Nov 3 17:53:36 2011 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f files/benx.mod.pdb -water tip3p -p system.top -o system.pdb -ff prot36-cgenff 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | BENX 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 BENX rtp BENX q 0.0 25 | 1 CG2R61 1 BENX CG 1 -0.115 12.011 ; qtot -0.115 26 | 2 HGR61 1 BENX HG 1 0.115 1.008 ; qtot 0 27 | 3 CG2R61 1 BENX CD1 1 -0.115 12.011 ; qtot -0.115 28 | 4 HGR61 1 BENX HD1 1 0.115 1.008 ; qtot 0 29 | 5 CG2R61 1 BENX CD2 1 -0.115 12.011 ; qtot -0.115 30 | 6 HGR61 1 BENX HD2 1 0.115 1.008 ; qtot 0 31 | 7 CG2R61 1 BENX CE1 1 -0.115 12.011 ; qtot -0.115 32 | 8 HGR61 1 BENX HE1 1 0.115 1.008 ; qtot 0 33 | 9 CG2R61 1 BENX CE2 1 -0.115 12.011 ; qtot -0.115 34 | 10 HGR61 1 BENX HE2 1 0.115 1.008 ; qtot 0 35 | 11 CG2R61 1 BENX CZ 1 -0.115 12.011 ; qtot -0.115 36 | 12 HGR61 1 BENX HZ 1 0.115 1.008 ; qtot 0 37 | 13 LP 1 BENX LPA 1 0.000 0.000 ; qtot 0 38 | 39 | [ bonds ] 40 | ; ai aj funct c0 c1 c2 c3 41 | 1 2 1 42 | 1 3 1 43 | 1 5 1 44 | 3 4 1 45 | 3 7 1 46 | 5 6 1 47 | 5 9 1 48 | 7 8 1 49 | 7 11 1 50 | 9 10 1 51 | 9 11 1 52 | 11 12 1 53 | 54 | [ pairs ] 55 | ; ai aj funct c0 c1 c2 c3 56 | 1 8 1 57 | 1 10 1 58 | 1 11 1 59 | 2 4 1 60 | 2 6 1 61 | 2 7 1 62 | 2 9 1 63 | 3 6 1 64 | 3 9 1 65 | 3 12 1 66 | 4 5 1 67 | 4 8 1 68 | 4 11 1 69 | 5 7 1 70 | 5 12 1 71 | 6 10 1 72 | 6 11 1 73 | 7 10 1 74 | 8 9 1 75 | 8 12 1 76 | 10 12 1 77 | 78 | [ angles ] 79 | ; ai aj ak funct c0 c1 c2 c3 80 | 2 1 3 5 81 | 2 1 5 5 82 | 3 1 5 5 83 | 1 3 4 5 84 | 1 3 7 5 85 | 4 3 7 5 86 | 1 5 6 5 87 | 1 5 9 5 88 | 6 5 9 5 89 | 3 7 8 5 90 | 3 7 11 5 91 | 8 7 11 5 92 | 5 9 10 5 93 | 5 9 11 5 94 | 10 9 11 5 95 | 7 11 9 5 96 | 7 11 12 5 97 | 9 11 12 5 98 | 99 | [ dihedrals ] 100 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 101 | 2 1 3 4 9 102 | 2 1 3 7 9 103 | 5 1 3 4 9 104 | 5 1 3 7 9 105 | 2 1 5 6 9 106 | 2 1 5 9 9 107 | 3 1 5 6 9 108 | 3 1 5 9 9 109 | 1 3 7 8 9 110 | 1 3 7 11 9 111 | 4 3 7 8 9 112 | 4 3 7 11 9 113 | 1 5 9 10 9 114 | 1 5 9 11 9 115 | 6 5 9 10 9 116 | 6 5 9 11 9 117 | 3 7 11 9 9 118 | 3 7 11 12 9 119 | 8 7 11 9 9 120 | 8 7 11 12 9 121 | 5 9 11 7 9 122 | 5 9 11 12 9 123 | 10 9 11 7 9 124 | 10 9 11 12 9 125 | 126 | 127 | [ virtual_sites2 ] 128 | ; Vsite from funct a 129 | 13 1 11 1 0.500 130 | 131 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/benx.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 11/ 3/11 18: 5:14 CREATED BY USER: prabhu 3 | ATOM 1 CG BENX 1 -0.013 -0.023 0.000 1.00 0.00 BENX 4 | ATOM 2 HG BENX 1 -0.554 -0.959 0.000 1.00 0.00 BENX 5 | ATOM 3 CD1 BENX 1 1.388 -0.023 0.000 1.00 0.00 BENX 6 | ATOM 4 HD1 BENX 1 1.929 -0.959 0.000 1.00 0.00 BENX 7 | ATOM 5 CD2 BENX 1 -0.714 1.191 0.000 1.00 0.00 BENX 8 | ATOM 6 HD2 BENX 1 -1.795 1.191 0.000 1.00 0.00 BENX 9 | ATOM 7 CE1 BENX 1 2.089 1.191 0.000 1.00 0.00 BENX 10 | ATOM 8 HE1 BENX 1 3.170 1.191 0.000 1.00 0.00 BENX 11 | ATOM 9 CE2 BENX 1 -0.013 2.405 0.000 1.00 0.00 BENX 12 | ATOM 10 HE2 BENX 1 -0.554 3.340 0.000 1.00 0.00 BENX 13 | ATOM 11 CZ BENX 1 1.388 2.405 0.000 1.00 0.00 BENX 14 | ATOM 12 HZ BENX 1 1.929 3.340 0.000 1.00 0.00 BENX 15 | ATOM 13 LPA BENX 1 0.674 1.168 0.000 1.00 0.00 BENX 16 | TER 14 BENX 1 17 | END 18 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/benz.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'benz.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Thu Apr 19 15:15:21 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f benz.pdb -p benz.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | BENZ 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 BENZ rtp BENZ q 0.0 25 | 1 CG2R61 1 BENZ CG 1 -0.115 12.011 ; qtot -0.115 26 | 2 HGR61 1 BENZ HG 1 0.115 1.008 ; qtot 0 27 | 3 CG2R61 1 BENZ CD1 1 -0.115 12.011 ; qtot -0.115 28 | 4 HGR61 1 BENZ HD1 1 0.115 1.008 ; qtot 0 29 | 5 CG2R61 1 BENZ CD2 1 -0.115 12.011 ; qtot -0.115 30 | 6 HGR61 1 BENZ HD2 1 0.115 1.008 ; qtot 0 31 | 7 CG2R61 1 BENZ CE1 1 -0.115 12.011 ; qtot -0.115 32 | 8 HGR61 1 BENZ HE1 1 0.115 1.008 ; qtot 0 33 | 9 CG2R61 1 BENZ CE2 1 -0.115 12.011 ; qtot -0.115 34 | 10 HGR61 1 BENZ HE2 1 0.115 1.008 ; qtot 0 35 | 11 CG2R61 1 BENZ CZ 1 -0.115 12.011 ; qtot -0.115 36 | 12 HGR61 1 BENZ HZ 1 0.115 1.008 ; qtot 0 37 | 38 | [ bonds ] 39 | ; ai aj funct c0 c1 c2 c3 40 | 1 2 1 41 | 1 3 1 42 | 1 5 1 43 | 3 4 1 44 | 3 7 1 45 | 5 6 1 46 | 5 9 1 47 | 7 8 1 48 | 7 11 1 49 | 9 10 1 50 | 9 11 1 51 | 11 12 1 52 | 53 | [ pairs ] 54 | ; ai aj funct c0 c1 c2 c3 55 | 1 8 1 56 | 1 10 1 57 | 1 11 1 58 | 2 4 1 59 | 2 6 1 60 | 2 7 1 61 | 2 9 1 62 | 3 6 1 63 | 3 9 1 64 | 3 12 1 65 | 4 5 1 66 | 4 8 1 67 | 4 11 1 68 | 5 7 1 69 | 5 12 1 70 | 6 10 1 71 | 6 11 1 72 | 7 10 1 73 | 8 9 1 74 | 8 12 1 75 | 10 12 1 76 | 77 | [ angles ] 78 | ; ai aj ak funct c0 c1 c2 c3 79 | 2 1 3 5 80 | 2 1 5 5 81 | 3 1 5 5 82 | 1 3 4 5 83 | 1 3 7 5 84 | 4 3 7 5 85 | 1 5 6 5 86 | 1 5 9 5 87 | 6 5 9 5 88 | 3 7 8 5 89 | 3 7 11 5 90 | 8 7 11 5 91 | 5 9 10 5 92 | 5 9 11 5 93 | 10 9 11 5 94 | 7 11 9 5 95 | 7 11 12 5 96 | 9 11 12 5 97 | 98 | [ dihedrals ] 99 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 100 | 2 1 3 4 9 101 | 2 1 3 7 9 102 | 5 1 3 4 9 103 | 5 1 3 7 9 104 | 2 1 5 6 9 105 | 2 1 5 9 9 106 | 3 1 5 6 9 107 | 3 1 5 9 9 108 | 1 3 7 8 9 109 | 1 3 7 11 9 110 | 4 3 7 8 9 111 | 4 3 7 11 9 112 | 1 5 9 10 9 113 | 1 5 9 11 9 114 | 6 5 9 10 9 115 | 6 5 9 11 9 116 | 3 7 11 9 9 117 | 3 7 11 12 9 118 | 8 7 11 9 9 119 | 8 7 11 12 9 120 | 5 9 11 7 9 121 | 5 9 11 12 9 122 | 10 9 11 7 9 123 | 10 9 11 12 9 124 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/benz.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 4/19/12 20:46: 4 CREATED BY USER: prabhu 3 | ATOM 1 CG BENZ 1 -0.013 -0.023 0.000 1.00 0.00 BENZ 4 | ATOM 2 HG BENZ 1 -0.554 -0.959 0.000 1.00 0.00 BENZ 5 | ATOM 3 CD1 BENZ 1 1.388 -0.023 0.000 1.00 0.00 BENZ 6 | ATOM 4 HD1 BENZ 1 1.929 -0.959 0.000 1.00 0.00 BENZ 7 | ATOM 5 CD2 BENZ 1 -0.714 1.191 -0.000 1.00 0.00 BENZ 8 | ATOM 6 HD2 BENZ 1 -1.795 1.191 -0.000 1.00 0.00 BENZ 9 | ATOM 7 CE1 BENZ 1 2.089 1.191 0.000 1.00 0.00 BENZ 10 | ATOM 8 HE1 BENZ 1 3.170 1.191 0.000 1.00 0.00 BENZ 11 | ATOM 9 CE2 BENZ 1 -0.013 2.405 -0.000 1.00 0.00 BENZ 12 | ATOM 10 HE2 BENZ 1 -0.554 3.340 -0.000 1.00 0.00 BENZ 13 | ATOM 11 CZ BENZ 1 1.388 2.405 -0.000 1.00 0.00 BENZ 14 | ATOM 12 HZ BENZ 1 1.929 3.340 -0.000 1.00 0.00 BENZ 15 | TER 13 BENZ 1 16 | END 17 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/brob.itp: -------------------------------------------------------------------------------- 1 | ; Created by atomgroup.write_gmx.itp() 2 | 3 | [ moleculetype ] 4 | ; Name nrexcl 5 | BROB 3 6 | 7 | [ atoms ] 8 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 9 | ; residue 1 BROB rtp BROB q qsum 10 | 1 CG2R61 1 BROB C1 1 -0.060 12.011 ; 11 | 2 HGR62 1 BROB H1 2 0.150 1.008 ; 12 | 3 CG2R61 1 BROB C2 3 -0.115 12.011 ; 13 | 4 HGR61 1 BROB H2 4 0.115 1.008 ; 14 | 5 CG2R61 1 BROB C3 5 -0.115 12.011 ; 15 | 6 HGR61 1 BROB H3 6 0.115 1.008 ; 16 | 7 CG2R61 1 BROB C4 7 -0.115 12.011 ; 17 | 8 HGR61 1 BROB H4 8 0.115 1.008 ; 18 | 9 CG2R61 1 BROB C5 9 -0.060 12.011 ; 19 | 10 HGR62 1 BROB H5 10 0.150 1.008 ; 20 | 11 CG2R61 1 BROB C6 11 -0.080 12.011 ; 21 | 12 BRGR1 1 BROB BR 12 -0.100 79.904 ; 22 | 23 | [ bonds ] 24 | ; ai aj funct c0 c1 c2 c3 25 | 1 2 1 26 | 1 3 1 27 | 1 11 1 28 | 3 4 1 29 | 3 5 1 30 | 5 6 1 31 | 5 7 1 32 | 7 9 1 33 | 7 8 1 34 | 9 10 1 35 | 9 11 1 36 | 11 12 1 37 | 38 | [ pairs ] 39 | ; ai aj funct c0 c1 c2 c3 40 | 1 10 1 41 | 1 6 1 42 | 1 7 1 43 | 2 9 1 44 | 2 12 1 45 | 2 4 1 46 | 2 5 1 47 | 3 9 1 48 | 3 12 1 49 | 3 8 1 50 | 4 11 1 51 | 4 6 1 52 | 4 7 1 53 | 5 11 1 54 | 5 10 1 55 | 6 9 1 56 | 6 8 1 57 | 7 12 1 58 | 8 10 1 59 | 8 11 1 60 | 10 12 1 61 | 62 | [ angles ] 63 | ; ai aj ak funct c0 c1 c2 c3 64 | 2 1 3 5 65 | 2 1 11 5 66 | 3 1 11 5 67 | 1 3 4 5 68 | 1 3 5 5 69 | 4 3 5 5 70 | 3 5 6 5 71 | 3 5 7 5 72 | 6 5 7 5 73 | 9 7 5 5 74 | 9 7 8 5 75 | 5 7 8 5 76 | 10 9 11 5 77 | 10 9 7 5 78 | 11 9 7 5 79 | 9 11 1 5 80 | 9 11 12 5 81 | 1 11 12 5 82 | 83 | [ dihedrals ] 84 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 85 | 2 1 3 4 9 86 | 2 1 3 5 9 87 | 11 1 3 4 9 88 | 11 1 3 5 9 89 | 2 1 11 9 9 90 | 2 1 11 12 9 91 | 3 1 11 9 9 92 | 3 1 11 12 9 93 | 1 3 5 6 9 94 | 1 3 5 7 9 95 | 4 3 5 6 9 96 | 4 3 5 7 9 97 | 3 5 7 9 9 98 | 3 5 7 8 9 99 | 6 5 7 9 9 100 | 6 5 7 8 9 101 | 5 7 9 10 9 102 | 5 7 9 11 9 103 | 8 7 9 10 9 104 | 8 7 9 11 9 105 | 10 9 11 1 9 106 | 10 9 11 12 9 107 | 7 9 11 1 9 108 | 7 9 11 12 9 109 | 110 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/brob.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 9/10/12 11:19:58 CREATED BY USER: prabhu 3 | ATOM 1 C1 BROB 1 -0.013 -0.023 0.000 1.00 0.00 BROB 4 | ATOM 2 H1 BROB 1 -0.558 -0.954 -0.000 1.00 0.00 BROB 5 | ATOM 3 C2 BROB 1 1.389 -0.023 0.000 1.00 0.00 BROB 6 | ATOM 4 H2 BROB 1 1.928 -0.960 0.000 1.00 0.00 BROB 7 | ATOM 5 C3 BROB 1 2.091 1.191 0.000 1.00 0.00 BROB 8 | ATOM 6 H3 BROB 1 3.171 1.191 0.000 1.00 0.00 BROB 9 | ATOM 7 C4 BROB 1 1.389 2.405 0.000 1.00 0.00 BROB 10 | ATOM 8 H4 BROB 1 1.928 3.341 0.000 1.00 0.00 BROB 11 | ATOM 9 C5 BROB 1 -0.013 2.404 0.000 1.00 0.00 BROB 12 | ATOM 10 H5 BROB 1 -0.558 3.336 -0.000 1.00 0.00 BROB 13 | ATOM 11 C6 BROB 1 -0.713 1.191 -0.000 1.00 0.00 BROB 14 | ATOM 12 BR BROB 1 -2.615 1.191 -0.000 1.00 0.00 BROB 15 | TER 13 BROB 1 16 | END 17 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/chlb.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'chlb.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Fri Jun 29 14:54:11 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f chlb.pdb -p chlb.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | CHLB 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 CHLB rtp CHLB q 0.0 25 | 1 CG2R61 1 CHLB C1 1 -0.1 12.011 ; qtot -0.1 26 | 2 HGR62 1 CHLB H1 2 0.15 1.008 ; qtot 0.05 27 | 3 CG2R61 1 CHLB C2 3 -0.115 12.011 ; qtot -0.065 28 | 4 HGR61 1 CHLB H2 4 0.115 1.008 ; qtot 0.05 29 | 5 CG2R61 1 CHLB C3 5 -0.115 12.011 ; qtot -0.065 30 | 6 HGR61 1 CHLB H3 6 0.115 1.008 ; qtot 0.05 31 | 7 CG2R61 1 CHLB C4 7 -0.115 12.011 ; qtot -0.065 32 | 8 HGR61 1 CHLB H4 8 0.115 1.008 ; qtot 0.05 33 | 9 CG2R61 1 CHLB C5 9 -0.1 12.011 ; qtot -0.05 34 | 10 HGR62 1 CHLB H5 10 0.15 1.008 ; qtot 0.1 35 | 11 CG2R61 1 CHLB C6 11 0.03 12.011 ; qtot 0.13 36 | 12 CLGR1 1 CHLB CL 12 -0.13 35.453 ; qtot 0 37 | 38 | [ bonds ] 39 | ; ai aj funct c0 c1 c2 c3 40 | 1 2 1 41 | 1 3 1 42 | 1 11 1 43 | 3 4 1 44 | 3 5 1 45 | 5 6 1 46 | 5 7 1 47 | 7 8 1 48 | 7 9 1 49 | 9 10 1 50 | 9 11 1 51 | 11 12 1 52 | 53 | [ pairs ] 54 | ; ai aj funct c0 c1 c2 c3 55 | 1 6 1 56 | 1 7 1 57 | 1 10 1 58 | 2 4 1 59 | 2 5 1 60 | 2 9 1 61 | 2 12 1 62 | 3 8 1 63 | 3 9 1 64 | 3 12 1 65 | 4 6 1 66 | 4 7 1 67 | 4 11 1 68 | 5 10 1 69 | 5 11 1 70 | 6 8 1 71 | 6 9 1 72 | 7 12 1 73 | 8 10 1 74 | 8 11 1 75 | 10 12 1 76 | 77 | [ angles ] 78 | ; ai aj ak funct c0 c1 c2 c3 79 | 2 1 3 5 80 | 2 1 11 5 81 | 3 1 11 5 82 | 1 3 4 5 83 | 1 3 5 5 84 | 4 3 5 5 85 | 3 5 6 5 86 | 3 5 7 5 87 | 6 5 7 5 88 | 5 7 8 5 89 | 5 7 9 5 90 | 8 7 9 5 91 | 7 9 10 5 92 | 7 9 11 5 93 | 10 9 11 5 94 | 1 11 9 5 95 | 1 11 12 5 96 | 9 11 12 5 97 | 98 | [ dihedrals ] 99 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 100 | 2 1 3 4 9 101 | 2 1 3 5 9 102 | 11 1 3 4 9 103 | 11 1 3 5 9 104 | 2 1 11 9 9 105 | 2 1 11 12 9 106 | 3 1 11 9 9 107 | 3 1 11 12 9 108 | 1 3 5 6 9 109 | 1 3 5 7 9 110 | 4 3 5 6 9 111 | 4 3 5 7 9 112 | 3 5 7 8 9 113 | 3 5 7 9 9 114 | 6 5 7 8 9 115 | 6 5 7 9 9 116 | 5 7 9 10 9 117 | 5 7 9 11 9 118 | 8 7 9 10 9 119 | 8 7 9 11 9 120 | 7 9 11 1 9 121 | 7 9 11 12 9 122 | 10 9 11 1 9 123 | 10 9 11 12 9 124 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/chlb.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 12/13/11 16:55:28 CREATED BY USER: prabhu 3 | ATOM 1 C1 CHLB 1 -0.012 -0.022 0.000 1.00 0.00 CHLB 4 | ATOM 2 H1 CHLB 1 -0.560 -0.952 0.000 1.00 0.00 CHLB 5 | ATOM 3 C2 CHLB 1 1.390 -0.024 0.000 1.00 0.00 CHLB 6 | ATOM 4 H2 CHLB 1 1.929 -0.960 0.000 1.00 0.00 CHLB 7 | ATOM 5 C3 CHLB 1 2.090 1.191 0.000 1.00 0.00 CHLB 8 | ATOM 6 H3 CHLB 1 3.171 1.191 0.000 1.00 0.00 CHLB 9 | ATOM 7 C4 CHLB 1 1.390 2.405 0.000 1.00 0.00 CHLB 10 | ATOM 8 H4 CHLB 1 1.929 3.341 0.000 1.00 0.00 CHLB 11 | ATOM 9 C5 CHLB 1 -0.012 2.404 0.000 1.00 0.00 CHLB 12 | ATOM 10 H5 CHLB 1 -0.560 3.334 0.000 1.00 0.00 CHLB 13 | ATOM 11 C6 CHLB 1 -0.712 1.191 0.000 1.00 0.00 CHLB 14 | ATOM 12 CL CHLB 1 -2.451 1.191 0.000 1.00 0.00 CHLB 15 | TER 13 CHLB 1 16 | END 17 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/flub.itp: -------------------------------------------------------------------------------- 1 | ; Created by atomgroup.write_gmx.itp() 2 | 3 | [ moleculetype ] 4 | ; Name nrexcl 5 | FLUB 3 6 | 7 | [ atoms ] 8 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 9 | ; residue 1 FLUB rtp FLUB q qsum 10 | 1 CG2R61 1 FLUB C1 1 -0.100 12.011 ; 11 | 2 HGR62 1 FLUB H1 2 0.150 1.008 ; 12 | 3 CG2R61 1 FLUB C2 3 -0.115 12.011 ; 13 | 4 HGR61 1 FLUB H2 4 0.115 1.008 ; 14 | 5 CG2R61 1 FLUB C3 5 -0.115 12.011 ; 15 | 6 HGR61 1 FLUB H3 6 0.115 1.008 ; 16 | 7 CG2R61 1 FLUB C4 7 -0.115 12.011 ; 17 | 8 HGR61 1 FLUB H4 8 0.115 1.008 ; 18 | 9 CG2R61 1 FLUB C5 9 -0.100 12.011 ; 19 | 10 HGR62 1 FLUB H5 10 0.150 1.008 ; 20 | 11 CG2R66 1 FLUB C6 11 0.110 12.011 ; 21 | 12 FGR1 1 FLUB F6 12 -0.210 18.998 ; 22 | 23 | [ bonds ] 24 | ; ai aj funct c0 c1 c2 c3 25 | 1 2 1 26 | 1 3 1 27 | 1 11 1 28 | 3 4 1 29 | 3 5 1 30 | 5 6 1 31 | 5 7 1 32 | 7 9 1 33 | 7 8 1 34 | 9 10 1 35 | 9 11 1 36 | 11 12 1 37 | 38 | [ pairs ] 39 | ; ai aj funct c0 c1 c2 c3 40 | 1 10 1 41 | 1 6 1 42 | 1 7 1 43 | 2 9 1 44 | 2 12 1 45 | 2 4 1 46 | 2 5 1 47 | 3 9 1 48 | 3 12 1 49 | 3 8 1 50 | 4 11 1 51 | 4 6 1 52 | 4 7 1 53 | 5 11 1 54 | 5 10 1 55 | 6 9 1 56 | 6 8 1 57 | 7 12 1 58 | 8 10 1 59 | 8 11 1 60 | 10 12 1 61 | 62 | [ angles ] 63 | ; ai aj ak funct c0 c1 c2 c3 64 | 2 1 3 5 65 | 2 1 11 5 66 | 3 1 11 5 67 | 1 3 4 5 68 | 1 3 5 5 69 | 4 3 5 5 70 | 3 5 6 5 71 | 3 5 7 5 72 | 6 5 7 5 73 | 9 7 5 5 74 | 9 7 8 5 75 | 5 7 8 5 76 | 10 9 11 5 77 | 10 9 7 5 78 | 11 9 7 5 79 | 9 11 1 5 80 | 9 11 12 5 81 | 1 11 12 5 82 | 83 | [ dihedrals ] 84 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 85 | 2 1 3 4 9 86 | 2 1 3 5 9 87 | 11 1 3 4 9 88 | 11 1 3 5 9 89 | 2 1 11 9 9 90 | 2 1 11 12 9 91 | 3 1 11 9 9 92 | 3 1 11 12 9 93 | 1 3 5 6 9 94 | 1 3 5 7 9 95 | 4 3 5 6 9 96 | 4 3 5 7 9 97 | 3 5 7 9 9 98 | 3 5 7 8 9 99 | 6 5 7 9 9 100 | 6 5 7 8 9 101 | 5 7 9 10 9 102 | 5 7 9 11 9 103 | 8 7 9 10 9 104 | 8 7 9 11 9 105 | 10 9 11 1 9 106 | 10 9 11 12 9 107 | 7 9 11 1 9 108 | 7 9 11 12 9 109 | 110 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/flub.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 9/10/12 11:10:52 CREATED BY USER: prabhu 3 | ATOM 1 C1 FLUB 1 -0.011 -0.027 0.000 1.00 0.00 FLUB 4 | ATOM 2 H1 FLUB 1 -0.560 -0.956 0.000 1.00 0.00 FLUB 5 | ATOM 3 C2 FLUB 1 1.391 -0.026 0.000 1.00 0.00 FLUB 6 | ATOM 4 H2 FLUB 1 1.933 -0.960 0.000 1.00 0.00 FLUB 7 | ATOM 5 C3 FLUB 1 2.086 1.191 0.000 1.00 0.00 FLUB 8 | ATOM 6 H3 FLUB 1 3.167 1.192 0.000 1.00 0.00 FLUB 9 | ATOM 7 C4 FLUB 1 1.391 2.408 0.000 1.00 0.00 FLUB 10 | ATOM 8 H4 FLUB 1 1.933 3.343 0.000 1.00 0.00 FLUB 11 | ATOM 9 C5 FLUB 1 -0.012 2.409 0.000 1.00 0.00 FLUB 12 | ATOM 10 H5 FLUB 1 -0.561 3.338 0.000 1.00 0.00 FLUB 13 | ATOM 11 C6 FLUB 1 -0.686 1.191 -0.000 1.00 0.00 FLUB 14 | ATOM 12 F6 FLUB 1 -2.043 1.191 -0.000 1.00 0.00 FLUB 15 | TER 13 FLUB 1 16 | END 17 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/form.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'form.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Mon Feb 13 12:29:12 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f form.pdb -p form.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | FORM 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 FORM rtp FORM q 0.0 25 | 1 HGR52 1 FORM HA 1 0.08 1.008 ; qtot 0.08 26 | 2 CG2O1 1 FORM C 1 0.42 12.011 ; qtot 0.5 27 | 3 NG2S2 1 FORM N 1 -0.69 14.007 ; qtot -0.19 28 | 4 HGP1 1 FORM HC 1 0.35 1.008 ; qtot 0.16 29 | 5 HGP1 1 FORM HT 1 0.35 1.008 ; qtot 0.51 30 | 6 OG2D1 1 FORM O 1 -0.51 15.9994 ; qtot 0 31 | 32 | [ bonds ] 33 | ; ai aj funct c0 c1 c2 c3 34 | 1 2 1 35 | 2 3 1 36 | 2 6 1 37 | 3 4 1 38 | 3 5 1 39 | 40 | [ pairs ] 41 | ; ai aj funct c0 c1 c2 c3 42 | 1 4 1 43 | 1 5 1 44 | 4 6 1 45 | 5 6 1 46 | 47 | [ angles ] 48 | ; ai aj ak funct c0 c1 c2 c3 49 | 1 2 3 5 50 | 1 2 6 5 51 | 3 2 6 5 52 | 2 3 4 5 53 | 2 3 5 5 54 | 4 3 5 5 55 | 56 | [ dihedrals ] 57 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 58 | 1 2 3 4 9 59 | 1 2 3 5 9 60 | 6 2 3 4 9 61 | 6 2 3 5 9 62 | 63 | [ dihedrals ] 64 | ; ai aj ak al funct c0 c1 c2 c3 65 | 1 6 3 2 2 66 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/form.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 2/13/12 12:28: 4 CREATED BY USER: prabhu 3 | ATOM 1 HA FORM 1 1.773 -1.015 0.000 1.00 0.00 FORM 4 | ATOM 2 C FORM 1 1.344 -0.007 0.000 1.00 0.00 FORM 5 | ATOM 3 N FORM 1 -0.007 -0.013 0.000 1.00 0.00 FORM 6 | ATOM 4 HC FORM 1 -0.453 0.878 0.000 1.00 0.00 FORM 7 | ATOM 5 HT FORM 1 -0.514 -0.869 0.000 1.00 0.00 FORM 8 | ATOM 6 O FORM 1 1.993 1.036 0.000 1.00 0.00 FORM 9 | TER 7 FORM 1 10 | END 11 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/forx.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'form.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Mon Feb 13 12:29:12 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f form.pdb -p form.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | FORX 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 FORX rtp FORX q 0.0 25 | 1 HGR52 1 FORX HA 1 0.08 1.008 ; qtot 0.08 26 | 2 CG2O1 1 FORX C 1 0.42 12.011 ; qtot 0.5 27 | 3 NG2S2 1 FORX N 1 -0.69 14.007 ; qtot -0.19 28 | 4 HGP1 1 FORX HC 1 0.35 1.008 ; qtot 0.16 29 | 5 HGP1 1 FORX HT 1 0.35 1.008 ; qtot 0.51 30 | 6 OG2D1 1 FORX O 1 -0.51 15.9994 ; qtot 0 31 | 7 LP 1 FORX LPA 1 0.00 0.000 ; qtot 0 32 | 33 | [ bonds ] 34 | ; ai aj funct c0 c1 c2 c3 35 | 1 2 1 36 | 2 3 1 37 | 2 6 1 38 | 3 4 1 39 | 3 5 1 40 | 41 | [ pairs ] 42 | ; ai aj funct c0 c1 c2 c3 43 | 1 4 1 44 | 1 5 1 45 | 4 6 1 46 | 5 6 1 47 | 48 | [ angles ] 49 | ; ai aj ak funct c0 c1 c2 c3 50 | 1 2 3 5 51 | 1 2 6 5 52 | 3 2 6 5 53 | 2 3 4 5 54 | 2 3 5 5 55 | 4 3 5 5 56 | 57 | [ dihedrals ] 58 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 59 | 1 2 3 4 9 60 | 1 2 3 5 9 61 | 6 2 3 4 9 62 | 6 2 3 5 9 63 | 64 | [ dihedrals ] 65 | ; ai aj ak al funct c0 c1 c2 c3 66 | 1 6 3 2 2 67 | 68 | [ virtual_sites2 ] 69 | ; Vsite from funct a 70 | 7 2 3 1 0.5 71 | 72 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/forx.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 2/13/12 12:43:43 CREATED BY USER: prabhu 3 | ATOM 1 HA FORX 1 1.773 -1.015 0.000 1.00 0.00 FORX 4 | ATOM 2 C FORX 1 1.344 -0.007 0.000 1.00 0.00 FORX 5 | ATOM 3 N FORX 1 -0.007 -0.013 0.000 1.00 0.00 FORX 6 | ATOM 4 HC FORX 1 -0.453 0.878 0.000 1.00 0.00 FORX 7 | ATOM 5 HT FORX 1 -0.514 -0.869 0.000 1.00 0.00 FORX 8 | ATOM 6 O FORX 1 1.993 1.036 0.000 1.00 0.00 FORX 9 | ATOM 7 LPA FORX 1 1.288 0.076 0.000 1.00 0.00 FORX 10 | TER 8 FORX 1 11 | END 12 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/imia.itp: -------------------------------------------------------------------------------- 1 | ; Created by atomgroup.write_gmx.itp() 2 | 3 | [ moleculetype ] 4 | ; Name nrexcl 5 | IMIA 3 6 | 7 | [ atoms ] 8 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 9 | ; residue 1 IMIA rtp IMIA q qsum 10 | 1 CG2R51 1 IMIA CG 1 -0.050 12.011 ; 11 | 2 HGR52 1 IMIA HG 2 0.090 1.008 ; 12 | 3 CG2R51 1 IMIA CD2 3 0.220 12.011 ; 13 | 4 HGR52 1 IMIA HD2 4 0.100 1.008 ; 14 | 5 NG2R51 1 IMIA ND1 5 -0.360 14.007 ; 15 | 6 HGP1 1 IMIA HD1 6 0.320 1.008 ; 16 | 7 CG2R53 1 IMIA CE1 7 0.250 12.011 ; 17 | 8 HGR52 1 IMIA HE1 8 0.130 1.008 ; 18 | 9 NG2R50 1 IMIA NE2 9 -0.700 14.007 ; 19 | 20 | [ bonds ] 21 | ; ai aj funct c0 c1 c2 c3 22 | 1 2 1 23 | 1 3 1 24 | 1 5 1 25 | 3 9 1 26 | 3 4 1 27 | 5 6 1 28 | 5 7 1 29 | 7 9 1 30 | 7 8 1 31 | 32 | [ pairs ] 33 | ; ai aj funct c0 c1 c2 c3 34 | 1 8 1 35 | 2 9 1 36 | 2 4 1 37 | 2 6 1 38 | 2 7 1 39 | 3 6 1 40 | 3 8 1 41 | 4 5 1 42 | 4 7 1 43 | 6 9 1 44 | 6 8 1 45 | 46 | [ angles ] 47 | ; ai aj ak funct c0 c1 c2 c3 48 | 2 1 3 5 49 | 2 1 5 5 50 | 3 1 5 5 51 | 9 3 1 5 52 | 9 3 4 5 53 | 1 3 4 5 54 | 1 5 6 5 55 | 1 5 7 5 56 | 6 5 7 5 57 | 9 7 5 5 58 | 9 7 8 5 59 | 5 7 8 5 60 | 3 9 7 5 61 | 62 | [ dihedrals ] 63 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 64 | 2 1 3 9 9 65 | 2 1 3 4 9 66 | 5 1 3 9 9 67 | 5 1 3 4 9 68 | 2 1 5 6 9 69 | 2 1 5 7 9 70 | 3 1 5 6 9 71 | 3 1 5 7 9 72 | 1 3 9 7 9 73 | 4 3 9 7 9 74 | 1 5 7 9 9 75 | 1 5 7 8 9 76 | 6 5 7 9 9 77 | 6 5 7 8 9 78 | 5 7 9 3 9 79 | 8 7 9 3 9 80 | 81 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/imia.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 10/ 1/13 18: 4:39 CREATED BY USER: prabhu 3 | ATOM 1 CG IMIA 1 -0.052 -0.082 0.076 1.00 0.00 IMIA 4 | ATOM 2 HG IMIA 1 -0.739 -0.913 0.001 1.00 0.00 IMIA 5 | ATOM 3 CD2 IMIA 1 1.306 -0.083 0.169 1.00 0.00 IMIA 6 | ATOM 4 HD2 IMIA 1 1.998 -0.917 0.188 1.00 0.00 IMIA 7 | ATOM 5 ND1 IMIA 1 -0.430 1.243 0.096 1.00 0.00 IMIA 8 | ATOM 6 HD1 IMIA 1 -1.371 1.602 0.044 1.00 0.00 IMIA 9 | ATOM 7 CE1 IMIA 1 0.717 1.978 0.199 1.00 0.00 IMIA 10 | ATOM 8 HE1 IMIA 1 0.729 3.070 0.237 1.00 0.00 IMIA 11 | ATOM 9 NE2 IMIA 1 1.788 1.213 0.246 1.00 0.00 IMIA 12 | TER 10 IMIA 1 13 | END 14 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/iodb.itp: -------------------------------------------------------------------------------- 1 | ; Created by atomgroup.write_gmx.itp() 2 | 3 | [ moleculetype ] 4 | ; Name nrexcl 5 | IODB 3 6 | 7 | [ atoms ] 8 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 9 | ; residue 1 IODB rtp IODB q qsum 10 | 1 CG2R61 1 IODB C1 1 -0.060 12.011 ; 11 | 2 HGR62 1 IODB H1 2 0.140 1.008 ; 12 | 3 CG2R61 1 IODB C2 3 -0.115 12.011 ; 13 | 4 HGR61 1 IODB H2 4 0.115 1.008 ; 14 | 5 CG2R61 1 IODB C3 5 -0.115 12.011 ; 15 | 6 HGR61 1 IODB H3 6 0.115 1.008 ; 16 | 7 CG2R61 1 IODB C4 7 -0.115 12.011 ; 17 | 8 HGR61 1 IODB H4 8 0.115 1.008 ; 18 | 9 CG2R61 1 IODB C5 9 -0.060 12.011 ; 19 | 10 HGR62 1 IODB H5 10 0.140 1.008 ; 20 | 11 CG2R61 1 IODB C6 11 -0.080 12.011 ; 21 | 12 IGR1 1 IODB I6 12 -0.080 126.904 ; 22 | 23 | [ bonds ] 24 | ; ai aj funct c0 c1 c2 c3 25 | 1 2 1 26 | 1 3 1 27 | 1 11 1 28 | 3 4 1 29 | 3 5 1 30 | 5 6 1 31 | 5 7 1 32 | 7 9 1 33 | 7 8 1 34 | 9 10 1 35 | 9 11 1 36 | 11 12 1 37 | 38 | [ pairs ] 39 | ; ai aj funct c0 c1 c2 c3 40 | 1 10 1 41 | 1 6 1 42 | 1 7 1 43 | 2 9 1 44 | 2 12 1 45 | 2 4 1 46 | 2 5 1 47 | 3 9 1 48 | 3 12 1 49 | 3 8 1 50 | 4 11 1 51 | 4 6 1 52 | 4 7 1 53 | 5 11 1 54 | 5 10 1 55 | 6 9 1 56 | 6 8 1 57 | 7 12 1 58 | 8 10 1 59 | 8 11 1 60 | 10 12 1 61 | 62 | [ angles ] 63 | ; ai aj ak funct c0 c1 c2 c3 64 | 2 1 3 5 65 | 2 1 11 5 66 | 3 1 11 5 67 | 1 3 4 5 68 | 1 3 5 5 69 | 4 3 5 5 70 | 3 5 6 5 71 | 3 5 7 5 72 | 6 5 7 5 73 | 9 7 5 5 74 | 9 7 8 5 75 | 5 7 8 5 76 | 10 9 11 5 77 | 10 9 7 5 78 | 11 9 7 5 79 | 9 11 1 5 80 | 9 11 12 5 81 | 1 11 12 5 82 | 83 | [ dihedrals ] 84 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 85 | 2 1 3 4 9 86 | 2 1 3 5 9 87 | 11 1 3 4 9 88 | 11 1 3 5 9 89 | 2 1 11 9 9 90 | 2 1 11 12 9 91 | 3 1 11 9 9 92 | 3 1 11 12 9 93 | 1 3 5 6 9 94 | 1 3 5 7 9 95 | 4 3 5 6 9 96 | 4 3 5 7 9 97 | 3 5 7 9 9 98 | 3 5 7 8 9 99 | 6 5 7 9 9 100 | 6 5 7 8 9 101 | 5 7 9 10 9 102 | 5 7 9 11 9 103 | 8 7 9 10 9 104 | 8 7 9 11 9 105 | 10 9 11 1 9 106 | 10 9 11 12 9 107 | 7 9 11 1 9 108 | 7 9 11 12 9 109 | 110 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/iodb.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 9/10/12 11:26: 0 CREATED BY USER: prabhu 3 | ATOM 1 C1 IODB 1 -0.013 -0.023 0.000 1.00 0.00 IODB 4 | ATOM 2 H1 IODB 1 -0.558 -0.955 -0.000 1.00 0.00 IODB 5 | ATOM 3 C2 IODB 1 1.389 -0.023 0.000 1.00 0.00 IODB 6 | ATOM 4 H2 IODB 1 1.928 -0.960 0.000 1.00 0.00 IODB 7 | ATOM 5 C3 IODB 1 2.090 1.191 0.000 1.00 0.00 IODB 8 | ATOM 6 H3 IODB 1 3.171 1.191 0.000 1.00 0.00 IODB 9 | ATOM 7 C4 IODB 1 1.389 2.405 0.000 1.00 0.00 IODB 10 | ATOM 8 H4 IODB 1 1.928 3.341 0.000 1.00 0.00 IODB 11 | ATOM 9 C5 IODB 1 -0.013 2.404 0.000 1.00 0.00 IODB 12 | ATOM 10 H5 IODB 1 -0.558 3.336 -0.000 1.00 0.00 IODB 13 | ATOM 11 C6 IODB 1 -0.713 1.191 -0.000 1.00 0.00 IODB 14 | ATOM 12 I6 IODB 1 -2.827 1.191 -0.000 1.00 0.00 IODB 15 | TER 13 IODB 1 16 | END 17 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/mamm.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'mamm.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Mon Feb 13 11:47:25 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f mamm.pdb -p mamm.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | MAMM 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 MAMM rtp MAMM q +1.0 25 | 1 CG334 1 MAMM CE 1 0.16 12.011 ; qtot 0.16 26 | 2 NG3P3 1 MAMM NZ 1 -0.3 14.007 ; qtot -0.14 27 | 3 HGA3 1 MAMM HE1 1 0.05 1.008 ; qtot -0.09 28 | 4 HGA3 1 MAMM HE2 1 0.05 1.008 ; qtot -0.04 29 | 5 HGA3 1 MAMM HE3 1 0.05 1.008 ; qtot 0.01 30 | 6 HGP2 1 MAMM HZ1 1 0.33 1.008 ; qtot 0.34 31 | 7 HGP2 1 MAMM HZ2 1 0.33 1.008 ; qtot 0.67 32 | 8 HGP2 1 MAMM HZ3 1 0.33 1.008 ; qtot 1 33 | 34 | [ bonds ] 35 | ; ai aj funct c0 c1 c2 c3 36 | 1 2 1 37 | 1 3 1 38 | 1 4 1 39 | 1 5 1 40 | 2 6 1 41 | 2 7 1 42 | 2 8 1 43 | 44 | [ pairs ] 45 | ; ai aj funct c0 c1 c2 c3 46 | 3 6 1 47 | 3 7 1 48 | 3 8 1 49 | 4 6 1 50 | 4 7 1 51 | 4 8 1 52 | 5 6 1 53 | 5 7 1 54 | 5 8 1 55 | 56 | [ angles ] 57 | ; ai aj ak funct c0 c1 c2 c3 58 | 2 1 3 5 59 | 2 1 4 5 60 | 2 1 5 5 61 | 3 1 4 5 62 | 3 1 5 5 63 | 4 1 5 5 64 | 1 2 6 5 65 | 1 2 7 5 66 | 1 2 8 5 67 | 6 2 7 5 68 | 6 2 8 5 69 | 7 2 8 5 70 | 71 | [ dihedrals ] 72 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 73 | 3 1 2 6 9 74 | 3 1 2 7 9 75 | 3 1 2 8 9 76 | 4 1 2 6 9 77 | 4 1 2 7 9 78 | 4 1 2 8 9 79 | 5 1 2 6 9 80 | 5 1 2 7 9 81 | 5 1 2 8 9 82 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/mamm.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 2/13/12 11:46:18 CREATED BY USER: prabhu 3 | ATOM 1 CE MAMM 1 1.090 -0.004 0.000 1.00 0.00 MAMM 4 | ATOM 2 NZ MAMM 1 1.554 1.405 0.000 1.00 0.00 MAMM 5 | ATOM 3 HE1 MAMM 1 1.475 -0.514 0.909 1.00 0.00 MAMM 6 | ATOM 4 HE2 MAMM 1 1.475 -0.514 -0.909 1.00 0.00 MAMM 7 | ATOM 5 HE3 MAMM 1 -0.021 -0.021 0.000 1.00 0.00 MAMM 8 | ATOM 6 HZ1 MAMM 1 1.201 1.897 0.847 1.00 0.00 MAMM 9 | ATOM 7 HZ2 MAMM 1 1.201 1.897 -0.847 1.00 0.00 MAMM 10 | ATOM 8 HZ3 MAMM 1 2.595 1.438 0.000 1.00 0.00 MAMM 11 | TER 9 MAMM 1 12 | END 13 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/mamx.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'mamm.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Fri Feb 10 17:17:55 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f mamm_charmm.pdb -o mamm.pdb -p mamm.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | MAMX 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 MAMX rtp MAMX q +1.0 25 | 1 CG334 1 MAMX CE 1 0.16 12.011 ; qtot 0.16 26 | 2 NG3P3 1 MAMX NZ 1 -0.3 14.007 ; qtot -0.14 27 | 3 HGA3 1 MAMX HE1 1 0.05 1.008 ; qtot -0.09 28 | 4 HGA3 1 MAMX HE2 1 0.05 1.008 ; qtot -0.04 29 | 5 HGA3 1 MAMX HE3 1 0.05 1.008 ; qtot 0.01 30 | 6 HGP2 1 MAMX HZ1 1 0.33 1.008 ; qtot 0.34 31 | 7 HGP2 1 MAMX HZ2 1 0.33 1.008 ; qtot 0.67 32 | 8 HGP2 1 MAMX HZ3 1 0.33 1.008 ; qtot 1 33 | 9 LP 1 MAMX LPA 1 0.00 0.000 ; qtot 1 34 | 35 | [ bonds ] 36 | ; ai aj funct c0 c1 c2 c3 37 | 1 2 1 38 | 1 3 1 39 | 1 4 1 40 | 1 5 1 41 | 2 6 1 42 | 2 7 1 43 | 2 8 1 44 | 45 | [ pairs ] 46 | ; ai aj funct c0 c1 c2 c3 47 | 3 6 1 48 | 3 7 1 49 | 3 8 1 50 | 4 6 1 51 | 4 7 1 52 | 4 8 1 53 | 5 6 1 54 | 5 7 1 55 | 5 8 1 56 | 57 | [ angles ] 58 | ; ai aj ak funct c0 c1 c2 c3 59 | 2 1 3 5 60 | 2 1 4 5 61 | 2 1 5 5 62 | 3 1 4 5 63 | 3 1 5 5 64 | 4 1 5 5 65 | 1 2 6 5 66 | 1 2 7 5 67 | 1 2 8 5 68 | 6 2 7 5 69 | 6 2 8 5 70 | 7 2 8 5 71 | 72 | [ dihedrals ] 73 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 74 | 3 1 2 6 9 75 | 3 1 2 7 9 76 | 3 1 2 8 9 77 | 4 1 2 6 9 78 | 4 1 2 7 9 79 | 4 1 2 8 9 80 | 5 1 2 6 9 81 | 5 1 2 7 9 82 | 5 1 2 8 9 83 | 84 | [ virtual_sites2 ] 85 | ; Vsite from funct a 86 | 9 1 2 1 0.5 87 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/mamx.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 2/10/12 17:33:14 CREATED BY USER: prabhu 3 | ATOM 1 CE MAMX 1 1.090 -0.004 0.000 1.00 0.00 MAMX 4 | ATOM 2 NZ MAMX 1 1.554 1.405 0.000 1.00 0.00 MAMX 5 | ATOM 3 HE1 MAMX 1 1.475 -0.514 0.909 1.00 0.00 MAMX 6 | ATOM 4 HE2 MAMX 1 1.475 -0.514 -0.909 1.00 0.00 MAMX 7 | ATOM 5 HE3 MAMX 1 -0.021 -0.021 0.000 1.00 0.00 MAMX 8 | ATOM 6 HZ1 MAMX 1 1.201 1.897 0.847 1.00 0.00 MAMX 9 | ATOM 7 HZ2 MAMX 1 1.201 1.897 -0.847 1.00 0.00 MAMX 10 | ATOM 8 HZ3 MAMX 1 2.595 1.438 0.000 1.00 0.00 MAMX 11 | ATOM 9 LPA MAMX 1 1.611 1.448 0.070 1.00 0.00 MAMX 12 | TER 10 MAMX 1 13 | END 14 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/mamy.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'mamm.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Fri Feb 10 17:17:55 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f mamm_charmm.pdb -o mamm.pdb -p mamm.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | MAMY 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 MAMY rtp MAMY q +1.0 25 | 1 CG334 1 MAMY CE 1 0.16 12.011 ; qtot 0.16 26 | 2 NG3P3 1 MAMY NZ 1 -0.3 14.007 ; qtot -0.14 27 | 3 HGA3 1 MAMY HE1 1 0.05 1.008 ; qtot -0.09 28 | 4 HGA3 1 MAMY HE2 1 0.05 1.008 ; qtot -0.04 29 | 5 HGA3 1 MAMY HE3 1 0.05 1.008 ; qtot 0.01 30 | 6 HGP2 1 MAMY HZ1 1 0.33 1.008 ; qtot 0.34 31 | 7 HGP2 1 MAMY HZ2 1 0.33 1.008 ; qtot 0.67 32 | 8 HGP2 1 MAMY HZ3 1 0.33 1.008 ; qtot 1 33 | 9 LQ 1 MAMY LPA 1 0.00 0.000 ; qtot 1 34 | 35 | [ bonds ] 36 | ; ai aj funct c0 c1 c2 c3 37 | 1 2 1 38 | 1 3 1 39 | 1 4 1 40 | 1 5 1 41 | 2 6 1 42 | 2 7 1 43 | 2 8 1 44 | 45 | [ pairs ] 46 | ; ai aj funct c0 c1 c2 c3 47 | 3 6 1 48 | 3 7 1 49 | 3 8 1 50 | 4 6 1 51 | 4 7 1 52 | 4 8 1 53 | 5 6 1 54 | 5 7 1 55 | 5 8 1 56 | 57 | [ angles ] 58 | ; ai aj ak funct c0 c1 c2 c3 59 | 2 1 3 5 60 | 2 1 4 5 61 | 2 1 5 5 62 | 3 1 4 5 63 | 3 1 5 5 64 | 4 1 5 5 65 | 1 2 6 5 66 | 1 2 7 5 67 | 1 2 8 5 68 | 6 2 7 5 69 | 6 2 8 5 70 | 7 2 8 5 71 | 72 | [ dihedrals ] 73 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 74 | 3 1 2 6 9 75 | 3 1 2 7 9 76 | 3 1 2 8 9 77 | 4 1 2 6 9 78 | 4 1 2 7 9 79 | 4 1 2 8 9 80 | 5 1 2 6 9 81 | 5 1 2 7 9 82 | 5 1 2 8 9 83 | 84 | [ virtual_sites2 ] 85 | ; Vsite from funct a 86 | 9 1 2 1 0.5 87 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/mamy.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 2/10/12 17:33:14 CREATED BY USER: prabhu 3 | ATOM 1 CE MAMY 1 1.090 -0.004 0.000 1.00 0.00 MAMY 4 | ATOM 2 NZ MAMY 1 1.554 1.405 0.000 1.00 0.00 MAMY 5 | ATOM 3 HE1 MAMY 1 1.475 -0.514 0.909 1.00 0.00 MAMY 6 | ATOM 4 HE2 MAMY 1 1.475 -0.514 -0.909 1.00 0.00 MAMY 7 | ATOM 5 HE3 MAMY 1 -0.021 -0.021 0.000 1.00 0.00 MAMY 8 | ATOM 6 HZ1 MAMY 1 1.201 1.897 0.847 1.00 0.00 MAMY 9 | ATOM 7 HZ2 MAMY 1 1.201 1.897 -0.847 1.00 0.00 MAMY 10 | ATOM 8 HZ3 MAMY 1 2.595 1.438 0.000 1.00 0.00 MAMY 11 | ATOM 9 LPA MAMY 1 1.611 1.448 0.070 1.00 0.00 MAMY 12 | TER 10 MAMY 1 13 | END 14 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/meoh.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'meoh.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Mon Feb 13 11:25:14 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f meoh_charmm.pdb -p meoh.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | MEOH 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 MEOH rtp MEOH q 0.0 25 | 1 CG331 1 MEOH CB 1 -0.04 12.011 ; qtot -0.04 26 | 2 OG311 1 MEOH OG 1 -0.65 15.9994 ; qtot -0.69 27 | 3 HGP1 1 MEOH HG1 1 0.42 1.008 ; qtot -0.27 28 | 4 HGA3 1 MEOH HB1 1 0.09 1.008 ; qtot -0.18 29 | 5 HGA3 1 MEOH HB2 1 0.09 1.008 ; qtot -0.09 30 | 6 HGA3 1 MEOH HB3 1 0.09 1.008 ; qtot 0 31 | 32 | [ bonds ] 33 | ; ai aj funct c0 c1 c2 c3 34 | 1 2 1 35 | 1 4 1 36 | 1 5 1 37 | 1 6 1 38 | 2 3 1 39 | 40 | [ pairs ] 41 | ; ai aj funct c0 c1 c2 c3 42 | 3 4 1 43 | 3 5 1 44 | 3 6 1 45 | 46 | [ angles ] 47 | ; ai aj ak funct c0 c1 c2 c3 48 | 2 1 4 5 49 | 2 1 5 5 50 | 2 1 6 5 51 | 4 1 5 5 52 | 4 1 6 5 53 | 5 1 6 5 54 | 1 2 3 5 55 | 56 | [ dihedrals ] 57 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 58 | 4 1 2 3 9 59 | 5 1 2 3 9 60 | 6 1 2 3 9 61 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/meoh.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 2/13/12 11:21:53 CREATED BY USER: prabhu 3 | ATOM 1 CB MEOH 1 1.358 1.366 0.000 1.00 0.00 MEOH 4 | ATOM 2 OG MEOH 1 0.951 -0.001 0.000 1.00 0.00 MEOH 5 | ATOM 3 HG1 MEOH 1 -0.011 -0.027 0.000 1.00 0.00 MEOH 6 | ATOM 4 HB1 MEOH 1 2.469 1.423 0.000 1.00 0.00 MEOH 7 | ATOM 5 HB2 MEOH 1 0.977 1.886 0.907 1.00 0.00 MEOH 8 | ATOM 6 HB3 MEOH 1 0.977 1.886 -0.907 1.00 0.00 MEOH 9 | TER 7 MEOH 1 10 | END 11 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/meox.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'meoh.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Mon Feb 13 11:25:14 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f meoh_charmm.pdb -p meoh.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | MEOX 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 MEOX rtp MEOX q 0.0 25 | 1 CG331 1 MEOX CB 1 -0.04 12.011 ; qtot -0.04 26 | 2 OG311 1 MEOX OG 1 -0.65 15.9994 ; qtot -0.69 27 | 3 HGP1 1 MEOX HG1 1 0.42 1.008 ; qtot -0.27 28 | 4 HGA3 1 MEOX HB1 1 0.09 1.008 ; qtot -0.18 29 | 5 HGA3 1 MEOX HB2 1 0.09 1.008 ; qtot -0.09 30 | 6 HGA3 1 MEOX HB3 1 0.09 1.008 ; qtot 0 31 | 7 LP 1 MEOX LPA 1 0.00 0.000 ; qtot 0 32 | 33 | [ bonds ] 34 | ; ai aj funct c0 c1 c2 c3 35 | 1 2 1 36 | 1 4 1 37 | 1 5 1 38 | 1 6 1 39 | 2 3 1 40 | 41 | [ pairs ] 42 | ; ai aj funct c0 c1 c2 c3 43 | 3 4 1 44 | 3 5 1 45 | 3 6 1 46 | 47 | [ angles ] 48 | ; ai aj ak funct c0 c1 c2 c3 49 | 2 1 4 5 50 | 2 1 5 5 51 | 2 1 6 5 52 | 4 1 5 5 53 | 4 1 6 5 54 | 5 1 6 5 55 | 1 2 3 5 56 | 57 | [ dihedrals ] 58 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 59 | 4 1 2 3 9 60 | 5 1 2 3 9 61 | 6 1 2 3 9 62 | 63 | [ virtual_sites2 ] 64 | ; Vsite from funct a 65 | 7 1 2 1 0.5 66 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/meox.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 2/13/12 12: 1:45 CREATED BY USER: prabhu 3 | ATOM 1 CB MEOX 1 1.358 1.366 0.000 1.00 0.00 MEOX 4 | ATOM 2 OG MEOX 1 0.951 -0.001 0.000 1.00 0.00 MEOX 5 | ATOM 3 HG1 MEOX 1 -0.011 -0.027 0.000 1.00 0.00 MEOX 6 | ATOM 4 HB1 MEOX 1 2.469 1.423 0.000 1.00 0.00 MEOX 7 | ATOM 5 HB2 MEOX 1 0.977 1.886 0.907 1.00 0.00 MEOX 8 | ATOM 6 HB3 MEOX 1 0.977 1.886 -0.907 1.00 0.00 MEOX 9 | ATOM 7 LPA MEOX 1 0.990 -0.093 0.000 1.00 0.00 MEOX 10 | TER 8 MEOX 1 11 | END 12 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/mqtr/benz.mqtr: -------------------------------------------------------------------------------- 1 | 12 2 | 1 CG BENZ 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 -0.013 -0.023 0.000 3 | 2 HG BENZ 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 -0.554 -0.959 0.000 4 | 3 CD1 BENZ 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 1.388 -0.023 0.000 5 | 4 HD1 BENZ 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 1.929 -0.959 0.000 6 | 5 CD2 BENZ 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 -0.714 1.191 -0.000 7 | 6 HD2 BENZ 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 -1.795 1.191 -0.000 8 | 7 CE1 BENZ 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 2.089 1.191 0.000 9 | 8 HE1 BENZ 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 3.170 1.191 0.000 10 | 9 CE2 BENZ 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 -0.013 2.405 -0.000 11 | 10 HE2 BENZ 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 -0.554 3.340 -0.000 12 | 11 CZ BENZ 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 1.388 2.405 -0.000 13 | 12 HZ BENZ 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 1.929 3.340 -0.000 14 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/mqtr/chlb.mqtr: -------------------------------------------------------------------------------- 1 | 12 2 | 1 C1 CHLB 1 1 12.011000 -0.100000 CG2R61 -0.070000 1.992400 -0.012 -0.022 0.000 3 | 2 H1 CHLB 1 1 1.008000 0.150000 HGR62 -0.046000 1.100000 -0.560 -0.952 -0.000 4 | 3 C2 CHLB 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 1.390 -0.024 0.000 5 | 4 H2 CHLB 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 1.929 -0.960 -0.000 6 | 5 C3 CHLB 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 2.090 1.191 0.000 7 | 6 H3 CHLB 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 3.171 1.191 -0.000 8 | 7 C4 CHLB 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 1.390 2.405 -0.000 9 | 8 H4 CHLB 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 1.929 3.341 0.000 10 | 9 C5 CHLB 1 1 12.011000 -0.100000 CG2R61 -0.070000 1.992400 -0.012 2.404 -0.000 11 | 10 H5 CHLB 1 1 1.008000 0.150000 HGR62 -0.046000 1.100000 -0.560 3.334 0.000 12 | 11 C6 CHLB 1 1 12.011000 0.030000 CG2R61 -0.070000 1.992400 -0.712 1.191 0.000 13 | 12 CL CHLB 1 1 35.453000 -0.130000 CLGR1 -0.320000 1.930000 -2.451 1.191 0.000 14 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/mqtr/tolu.mqtr: -------------------------------------------------------------------------------- 1 | 15 2 | 1 CG TOLU 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 -0.001 -0.002 -0.002 3 | 2 HG TOLU 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 -0.541 -0.938 -0.005 4 | 3 CD1 TOLU 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 1.400 -0.002 -0.000 5 | 4 HD1 TOLU 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 1.941 -0.938 -0.004 6 | 5 CD2 TOLU 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 -0.702 1.212 -0.000 7 | 6 HD2 TOLU 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 -1.782 1.212 -0.004 8 | 7 CE1 TOLU 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 2.100 1.212 0.003 9 | 8 HE1 TOLU 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 3.180 1.214 0.002 10 | 9 CE2 TOLU 1 1 12.011000 -0.115000 CG2R61 -0.070000 1.992400 -0.000 2.425 0.003 11 | 10 HE2 TOLU 1 1 1.008000 0.115000 HGR61 -0.030000 1.358200 -0.538 3.361 0.002 12 | 11 CZ TOLU 1 1 12.011000 0.000000 CG2R61 -0.070000 1.992400 1.403 2.430 0.010 13 | 12 CT TOLU 1 1 12.011000 -0.270000 CG331 -0.078000 2.050000 2.151 3.726 0.002 14 | 13 H11 TOLU 1 1 1.008000 0.090000 HGA3 -0.024000 1.340000 2.326 4.029 -1.053 15 | 14 H12 TOLU 1 1 1.008000 0.090000 HGA3 -0.024000 1.340000 3.124 3.599 0.524 16 | 15 H13 TOLU 1 1 1.008000 0.090000 HGA3 -0.024000 1.340000 1.555 4.505 0.524 17 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/phen.itp: -------------------------------------------------------------------------------- 1 | ; Created by atomgroup.write_gmx.itp() 2 | 3 | [ moleculetype ] 4 | ; Name nrexcl 5 | PHEN 3 6 | 7 | [ atoms ] 8 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 9 | ; residue 1 PHEN rtp PHEN q qsum 10 | 1 CG2R61 1 PHEN CG 1 -0.115 12.011 ; 11 | 2 HGR61 1 PHEN HG 2 0.115 1.008 ; 12 | 3 CG2R61 1 PHEN CD1 3 -0.115 12.011 ; 13 | 4 HGR61 1 PHEN HD1 4 0.115 1.008 ; 14 | 5 CG2R61 1 PHEN CD2 5 -0.115 12.011 ; 15 | 6 HGR61 1 PHEN HD2 6 0.115 1.008 ; 16 | 7 CG2R61 1 PHEN CE1 7 -0.115 12.011 ; 17 | 8 HGR61 1 PHEN HE1 8 0.115 1.008 ; 18 | 9 CG2R61 1 PHEN CE2 9 -0.115 12.011 ; 19 | 10 HGR61 1 PHEN HE2 10 0.115 1.008 ; 20 | 11 CG2R61 1 PHEN CZ 11 0.110 12.011 ; 21 | 12 OG311 1 PHEN OH 12 -0.530 15.999 ; 22 | 13 HGP1 1 PHEN HH 13 0.420 1.008 ; 23 | 24 | [ bonds ] 25 | ; ai aj funct c0 c1 c2 c3 26 | 1 2 1 27 | 1 3 1 28 | 1 5 1 29 | 3 4 1 30 | 3 7 1 31 | 5 9 1 32 | 5 6 1 33 | 7 11 1 34 | 7 8 1 35 | 9 10 1 36 | 9 11 1 37 | 11 12 1 38 | 12 13 1 39 | 40 | [ pairs ] 41 | ; ai aj funct c0 c1 c2 c3 42 | 1 10 1 43 | 1 11 1 44 | 1 8 1 45 | 2 9 1 46 | 2 4 1 47 | 2 6 1 48 | 2 7 1 49 | 3 9 1 50 | 3 12 1 51 | 3 6 1 52 | 4 11 1 53 | 4 5 1 54 | 4 8 1 55 | 5 12 1 56 | 5 7 1 57 | 6 11 1 58 | 6 10 1 59 | 7 13 1 60 | 7 10 1 61 | 8 9 1 62 | 8 12 1 63 | 9 13 1 64 | 10 12 1 65 | 66 | [ angles ] 67 | ; ai aj ak funct c0 c1 c2 c3 68 | 2 1 3 5 69 | 2 1 5 5 70 | 3 1 5 5 71 | 1 3 4 5 72 | 1 3 7 5 73 | 4 3 7 5 74 | 1 5 9 5 75 | 1 5 6 5 76 | 9 5 6 5 77 | 3 7 11 5 78 | 3 7 8 5 79 | 11 7 8 5 80 | 10 9 11 5 81 | 10 9 5 5 82 | 11 9 5 5 83 | 9 11 12 5 84 | 9 11 7 5 85 | 12 11 7 5 86 | 11 12 13 5 87 | 88 | [ dihedrals ] 89 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 90 | 2 1 3 4 9 91 | 2 1 3 7 9 92 | 5 1 3 4 9 93 | 5 1 3 7 9 94 | 2 1 5 9 9 95 | 2 1 5 6 9 96 | 3 1 5 9 9 97 | 3 1 5 6 9 98 | 1 3 7 11 9 99 | 1 3 7 8 9 100 | 4 3 7 11 9 101 | 4 3 7 8 9 102 | 1 5 9 10 9 103 | 1 5 9 11 9 104 | 6 5 9 10 9 105 | 6 5 9 11 9 106 | 3 7 11 9 9 107 | 3 7 11 12 9 108 | 8 7 11 9 9 109 | 8 7 11 12 9 110 | 10 9 11 12 9 111 | 10 9 11 7 9 112 | 5 9 11 12 9 113 | 5 9 11 7 9 114 | 9 11 12 13 9 115 | 7 11 12 13 9 116 | 117 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/phen.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 9/10/12 11:42: 7 CREATED BY USER: prabhu 3 | ATOM 1 CG PHEN 1 -0.014 -0.024 0.000 1.00 0.00 PHEN 4 | ATOM 2 HG PHEN 1 -0.553 -0.961 0.000 1.00 0.00 PHEN 5 | ATOM 3 CD1 PHEN 1 1.388 -0.024 0.000 1.00 0.00 PHEN 6 | ATOM 4 HD1 PHEN 1 1.930 -0.958 0.000 1.00 0.00 PHEN 7 | ATOM 5 CD2 PHEN 1 -0.716 1.189 -0.000 1.00 0.00 PHEN 8 | ATOM 6 HD2 PHEN 1 -1.797 1.187 -0.000 1.00 0.00 PHEN 9 | ATOM 7 CE1 PHEN 1 2.086 1.192 0.000 1.00 0.00 PHEN 10 | ATOM 8 HE1 PHEN 1 3.166 1.200 0.000 1.00 0.00 PHEN 11 | ATOM 9 CE2 PHEN 1 -0.015 2.405 -0.000 1.00 0.00 PHEN 12 | ATOM 10 HE2 PHEN 1 -0.561 3.335 -0.000 1.00 0.00 PHEN 13 | ATOM 11 CZ PHEN 1 1.386 2.404 -0.000 1.00 0.00 PHEN 14 | ATOM 12 OH PHEN 1 2.098 3.619 -0.000 1.00 0.00 PHEN 15 | ATOM 13 HH PHEN 1 1.456 4.330 -0.000 1.00 0.00 PHEN 16 | TER 14 PHEN 1 17 | END 18 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/prox.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'pro2.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Mon Feb 13 16:44:30 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f pro2.pdb -p pro2.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | PROX 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 PROX rtp PROX q 0.0 25 | 1 CG311 1 PROX C2 1 0.14 12.011 ; qtot 0.14 26 | 2 OG311 1 PROX O2 1 -0.65 15.9994 ; qtot -0.51 27 | 3 HGP1 1 PROX HO2 1 0.42 1.008 ; qtot -0.09 28 | 4 HGA1 1 PROX H21 1 0.09 1.008 ; qtot 0 29 | 5 CG331 1 PROX C1 1 -0.27 12.011 ; qtot -0.27 30 | 6 HGA3 1 PROX H11 1 0.09 1.008 ; qtot -0.18 31 | 7 HGA3 1 PROX H12 1 0.09 1.008 ; qtot -0.09 32 | 8 HGA3 1 PROX H13 1 0.09 1.008 ; qtot 0 33 | 9 CG331 1 PROX C3 1 -0.27 12.011 ; qtot -0.27 34 | 10 HGA3 1 PROX H31 1 0.09 1.008 ; qtot -0.18 35 | 11 HGA3 1 PROX H32 1 0.09 1.008 ; qtot -0.09 36 | 12 HGA3 1 PROX H33 1 0.09 1.008 ; qtot 0 37 | 13 LP 1 PROX LPA 1 0.00 0.000 ; qtot 0 38 | 39 | [ bonds ] 40 | ; ai aj funct c0 c1 c2 c3 41 | 1 2 1 42 | 1 4 1 43 | 1 5 1 44 | 1 9 1 45 | 2 3 1 46 | 5 6 1 47 | 5 7 1 48 | 5 8 1 49 | 9 10 1 50 | 9 11 1 51 | 9 12 1 52 | 53 | [ pairs ] 54 | ; ai aj funct c0 c1 c2 c3 55 | 2 6 1 56 | 2 7 1 57 | 2 8 1 58 | 2 10 1 59 | 2 11 1 60 | 2 12 1 61 | 3 4 1 62 | 3 5 1 63 | 3 9 1 64 | 4 6 1 65 | 4 7 1 66 | 4 8 1 67 | 4 10 1 68 | 4 11 1 69 | 4 12 1 70 | 5 10 1 71 | 5 11 1 72 | 5 12 1 73 | 6 9 1 74 | 7 9 1 75 | 8 9 1 76 | 77 | [ angles ] 78 | ; ai aj ak funct c0 c1 c2 c3 79 | 2 1 4 5 80 | 2 1 5 5 81 | 2 1 9 5 82 | 4 1 5 5 83 | 4 1 9 5 84 | 5 1 9 5 85 | 1 2 3 5 86 | 1 5 6 5 87 | 1 5 7 5 88 | 1 5 8 5 89 | 6 5 7 5 90 | 6 5 8 5 91 | 7 5 8 5 92 | 1 9 10 5 93 | 1 9 11 5 94 | 1 9 12 5 95 | 10 9 11 5 96 | 10 9 12 5 97 | 11 9 12 5 98 | 99 | [ dihedrals ] 100 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 101 | 4 1 2 3 9 102 | 5 1 2 3 9 103 | 9 1 2 3 9 104 | 2 1 5 6 9 105 | 2 1 5 7 9 106 | 2 1 5 8 9 107 | 4 1 5 6 9 108 | 4 1 5 7 9 109 | 4 1 5 8 9 110 | 9 1 5 6 9 111 | 9 1 5 7 9 112 | 9 1 5 8 9 113 | 2 1 9 10 9 114 | 2 1 9 11 9 115 | 2 1 9 12 9 116 | 4 1 9 10 9 117 | 4 1 9 11 9 118 | 4 1 9 12 9 119 | 5 1 9 10 9 120 | 5 1 9 11 9 121 | 5 1 9 12 9 122 | 123 | [ virtual_sites2 ] 124 | ; Vsite from funct a 125 | 13 2 1 1 0.99 126 | 127 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/prox.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 2/13/12 16:42:50 CREATED BY USER: prabhu 3 | ATOM 1 C2 PROX 1 1.532 -0.026 0.014 1.00 0.00 PROX 4 | ATOM 2 O2 PROX 1 1.956 -0.691 -1.158 1.00 0.00 PROX 5 | ATOM 3 HO2 PROX 1 1.603 -1.581 -1.100 1.00 0.00 PROX 6 | ATOM 4 H21 PROX 1 1.897 -0.583 0.910 1.00 0.00 PROX 7 | ATOM 5 C1 PROX 1 0.005 0.011 0.003 1.00 0.00 PROX 8 | ATOM 6 H11 PROX 1 -0.419 -1.015 0.007 1.00 0.00 PROX 9 | ATOM 7 H12 PROX 1 -0.358 0.542 -0.903 1.00 0.00 PROX 10 | ATOM 8 H13 PROX 1 -0.371 0.551 0.898 1.00 0.00 PROX 11 | ATOM 9 C3 PROX 1 2.142 1.374 0.001 1.00 0.00 PROX 12 | ATOM 10 H31 PROX 1 3.251 1.312 -0.021 1.00 0.00 PROX 13 | ATOM 11 H32 PROX 1 1.834 1.942 0.903 1.00 0.00 PROX 14 | ATOM 12 H33 PROX 1 1.806 1.930 -0.901 1.00 0.00 PROX 15 | ATOM 13 LPA PROX 1 1.478 0.058 0.013 1.00 0.00 PROX 16 | TER 14 PROX 1 17 | END 18 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/prpa.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'prpx.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Tue Nov 8 10:59:13 2011 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f files/prpx_nolp.pdb -water tip3p -p prpx.top -o prpx.pdb -ff prot36-cgenff -i prpx_posre.itp -v 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | PRPA 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 PRPA rtp PRPA q 0.0 25 | 1 HGA3 1 PRPA H11 1 0.09 1.008 ; qtot 0.09 26 | 2 HGA3 1 PRPA H12 1 0.09 1.008 ; qtot 0.18 27 | 3 HGA3 1 PRPA H13 1 0.09 1.008 ; qtot 0.27 28 | 4 CG331 1 PRPA C1 1 -0.27 12.011 ; qtot 0 29 | 5 CG321 1 PRPA C2 1 -0.18 12.011 ; qtot -0.18 30 | 6 HGA2 1 PRPA H21 1 0.09 1.008 ; qtot -0.09 31 | 7 HGA2 1 PRPA H22 1 0.09 1.008 ; qtot 0 32 | 8 HGA3 1 PRPA H31 1 0.09 1.008 ; qtot 0.09 33 | 9 HGA3 1 PRPA H32 1 0.09 1.008 ; qtot 0.18 34 | 10 HGA3 1 PRPA H33 1 0.09 1.008 ; qtot 0.27 35 | 11 CG331 1 PRPA C3 1 -0.27 12.011 ; qtot 0 36 | 37 | [ bonds ] 38 | ; ai aj funct c0 c1 c2 c3 39 | 1 4 1 40 | 2 4 1 41 | 3 4 1 42 | 4 5 1 43 | 5 6 1 44 | 5 7 1 45 | 5 11 1 46 | 8 11 1 47 | 9 11 1 48 | 10 11 1 49 | 50 | [ pairs ] 51 | ; ai aj funct c0 c1 c2 c3 52 | 1 6 1 53 | 1 7 1 54 | 1 11 1 55 | 2 6 1 56 | 2 7 1 57 | 2 11 1 58 | 3 6 1 59 | 3 7 1 60 | 3 11 1 61 | 4 8 1 62 | 4 9 1 63 | 4 10 1 64 | 6 8 1 65 | 6 9 1 66 | 6 10 1 67 | 7 8 1 68 | 7 9 1 69 | 7 10 1 70 | 71 | [ angles ] 72 | ; ai aj ak funct c0 c1 c2 c3 73 | 1 4 2 5 74 | 1 4 3 5 75 | 1 4 5 5 76 | 2 4 3 5 77 | 2 4 5 5 78 | 3 4 5 5 79 | 4 5 6 5 80 | 4 5 7 5 81 | 4 5 11 5 82 | 6 5 7 5 83 | 6 5 11 5 84 | 7 5 11 5 85 | 5 11 8 5 86 | 5 11 9 5 87 | 5 11 10 5 88 | 8 11 9 5 89 | 8 11 10 5 90 | 9 11 10 5 91 | 92 | [ dihedrals ] 93 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 94 | 1 4 5 6 9 95 | 1 4 5 7 9 96 | 1 4 5 11 9 97 | 2 4 5 6 9 98 | 2 4 5 7 9 99 | 2 4 5 11 9 100 | 3 4 5 6 9 101 | 3 4 5 7 9 102 | 3 4 5 11 9 103 | 4 5 11 8 9 104 | 4 5 11 9 9 105 | 4 5 11 10 9 106 | 6 5 11 8 9 107 | 6 5 11 9 9 108 | 6 5 11 10 9 109 | 7 5 11 8 9 110 | 7 5 11 9 9 111 | 7 5 11 10 9 112 | 113 | 114 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/prpa.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 11/ 8/11 10:56:41 CREATED BY USER: prabhu 3 | ATOM 1 H11 PRPA 1 -0.382 1.043 0.000 1.00 0.00 PRPA 4 | ATOM 2 H12 PRPA 1 -0.382 -0.522 -0.904 1.00 0.00 PRPA 5 | ATOM 3 H13 PRPA 1 -0.382 -0.522 0.904 1.00 0.00 PRPA 6 | ATOM 4 C1 PRPA 1 0.000 0.000 0.000 1.00 0.00 PRPA 7 | ATOM 5 C2 PRPA 1 1.528 0.000 0.000 1.00 0.00 PRPA 8 | ATOM 6 H21 PRPA 1 1.910 -0.522 0.904 1.00 0.00 PRPA 9 | ATOM 7 H22 PRPA 1 1.910 -0.522 -0.904 1.00 0.00 PRPA 10 | ATOM 8 H31 PRPA 1 1.352 2.169 0.000 1.00 0.00 PRPA 11 | ATOM 9 H32 PRPA 1 2.781 1.533 0.904 1.00 0.00 PRPA 12 | ATOM 10 H33 PRPA 1 2.781 1.533 -0.904 1.00 0.00 PRPA 13 | ATOM 11 C3 PRPA 1 2.149 1.396 0.000 1.00 0.00 PRPA 14 | TER 12 PRPA 1 15 | END 16 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/prpx.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'prpx.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Tue Nov 8 10:59:13 2011 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f files/prpx_nolp.pdb -water tip3p -p prpx.top -o prpx.pdb -ff prot36-cgenff -i prpx_posre.itp -v 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | PRPX 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 PRPX rtp PRPX q 0.0 25 | 1 HGA3 1 PRPX H11 1 0.09 1.008 ; qtot 0.09 26 | 2 HGA3 1 PRPX H12 1 0.09 1.008 ; qtot 0.18 27 | 3 HGA3 1 PRPX H13 1 0.09 1.008 ; qtot 0.27 28 | 4 CG331 1 PRPX C1 1 -0.27 12.011 ; qtot 0 29 | 5 CG321 1 PRPX C2 1 -0.18 12.011 ; qtot -0.18 30 | 6 HGA2 1 PRPX H21 1 0.09 1.008 ; qtot -0.09 31 | 7 HGA2 1 PRPX H22 1 0.09 1.008 ; qtot 0 32 | 8 HGA3 1 PRPX H31 1 0.09 1.008 ; qtot 0.09 33 | 9 HGA3 1 PRPX H32 1 0.09 1.008 ; qtot 0.18 34 | 10 HGA3 1 PRPX H33 1 0.09 1.008 ; qtot 0.27 35 | 11 CG331 1 PRPX C3 1 -0.27 12.011 ; qtot 0 36 | 12 LP 1 PRPX LPA 1 0.000 0.000 ; qtot 0 37 | 38 | [ bonds ] 39 | ; ai aj funct c0 c1 c2 c3 40 | 1 4 1 41 | 2 4 1 42 | 3 4 1 43 | 4 5 1 44 | 5 6 1 45 | 5 7 1 46 | 5 11 1 47 | 8 11 1 48 | 9 11 1 49 | 10 11 1 50 | 51 | [ pairs ] 52 | ; ai aj funct c0 c1 c2 c3 53 | 1 6 1 54 | 1 7 1 55 | 1 11 1 56 | 2 6 1 57 | 2 7 1 58 | 2 11 1 59 | 3 6 1 60 | 3 7 1 61 | 3 11 1 62 | 4 8 1 63 | 4 9 1 64 | 4 10 1 65 | 6 8 1 66 | 6 9 1 67 | 6 10 1 68 | 7 8 1 69 | 7 9 1 70 | 7 10 1 71 | 72 | [ angles ] 73 | ; ai aj ak funct c0 c1 c2 c3 74 | 1 4 2 5 75 | 1 4 3 5 76 | 1 4 5 5 77 | 2 4 3 5 78 | 2 4 5 5 79 | 3 4 5 5 80 | 4 5 6 5 81 | 4 5 7 5 82 | 4 5 11 5 83 | 6 5 7 5 84 | 6 5 11 5 85 | 7 5 11 5 86 | 5 11 8 5 87 | 5 11 9 5 88 | 5 11 10 5 89 | 8 11 9 5 90 | 8 11 10 5 91 | 9 11 10 5 92 | 93 | [ dihedrals ] 94 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 95 | 1 4 5 6 9 96 | 1 4 5 7 9 97 | 1 4 5 11 9 98 | 2 4 5 6 9 99 | 2 4 5 7 9 100 | 2 4 5 11 9 101 | 3 4 5 6 9 102 | 3 4 5 7 9 103 | 3 4 5 11 9 104 | 4 5 11 8 9 105 | 4 5 11 9 9 106 | 4 5 11 10 9 107 | 6 5 11 8 9 108 | 6 5 11 9 9 109 | 6 5 11 10 9 110 | 7 5 11 8 9 111 | 7 5 11 9 9 112 | 7 5 11 10 9 113 | 114 | [ virtual_sites2 ] 115 | ; Vsite from funct a 116 | 12 4 5 1 0.95 117 | 118 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/prpx.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 11/ 8/11 10:56:41 CREATED BY USER: prabhu 3 | ATOM 1 H11 PRPX 1 -0.382 1.043 0.000 1.00 0.00 PRPX 4 | ATOM 2 H12 PRPX 1 -0.382 -0.522 -0.904 1.00 0.00 PRPX 5 | ATOM 3 H13 PRPX 1 -0.382 -0.522 0.904 1.00 0.00 PRPX 6 | ATOM 4 C1 PRPX 1 0.000 0.000 0.000 1.00 0.00 PRPX 7 | ATOM 5 C2 PRPX 1 1.528 0.000 0.000 1.00 0.00 PRPX 8 | ATOM 6 H21 PRPX 1 1.910 -0.522 0.904 1.00 0.00 PRPX 9 | ATOM 7 H22 PRPX 1 1.910 -0.522 -0.904 1.00 0.00 PRPX 10 | ATOM 8 H31 PRPX 1 1.352 2.169 0.000 1.00 0.00 PRPX 11 | ATOM 9 H32 PRPX 1 2.781 1.533 0.904 1.00 0.00 PRPX 12 | ATOM 10 H33 PRPX 1 2.781 1.533 -0.904 1.00 0.00 PRPX 13 | ATOM 11 C3 PRPX 1 2.149 1.396 0.000 1.00 0.00 PRPX 14 | ATOM 12 LPA PRPX 1 1.474 0.084 0.000 1.00 0.00 PRPX 15 | TER 13 PRPX 1 16 | END 17 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/pyr1.itp: -------------------------------------------------------------------------------- 1 | ; Created by atomgroup.write_gmx.itp() 2 | 3 | [ moleculetype ] 4 | ; Name nrexcl 5 | PYR1 3 6 | 7 | [ atoms ] 8 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 9 | ; residue 1 PYR1 rtp PYR1 q qsum 10 | 1 NG2R60 1 PYR1 N1 1 -0.600 14.007 ; 11 | 2 CG2R61 1 PYR1 C2 2 0.180 12.011 ; 12 | 3 CG2R61 1 PYR1 C3 3 -0.115 12.011 ; 13 | 4 CG2R61 1 PYR1 C4 4 -0.115 12.011 ; 14 | 5 CG2R61 1 PYR1 C5 5 -0.115 12.011 ; 15 | 6 CG2R61 1 PYR1 C6 6 0.180 12.011 ; 16 | 7 HGR62 1 PYR1 H2 7 0.120 1.008 ; 17 | 8 HGR61 1 PYR1 H3 8 0.115 1.008 ; 18 | 9 HGR61 1 PYR1 H4 9 0.115 1.008 ; 19 | 10 HGR61 1 PYR1 H5 10 0.115 1.008 ; 20 | 11 HGR62 1 PYR1 H6 11 0.120 1.008 ; 21 | 22 | [ bonds ] 23 | ; ai aj funct c0 c1 c2 c3 24 | 1 2 1 25 | 1 6 1 26 | 2 3 1 27 | 2 7 1 28 | 3 4 1 29 | 3 8 1 30 | 4 9 1 31 | 4 5 1 32 | 5 10 1 33 | 5 6 1 34 | 6 11 1 35 | 36 | [ pairs ] 37 | ; ai aj funct c0 c1 c2 c3 38 | 1 10 1 39 | 1 4 1 40 | 1 8 1 41 | 2 9 1 42 | 2 11 1 43 | 2 5 1 44 | 3 10 1 45 | 3 6 1 46 | 4 11 1 47 | 4 7 1 48 | 5 8 1 49 | 6 9 1 50 | 6 7 1 51 | 7 8 1 52 | 8 9 1 53 | 9 10 1 54 | 10 11 1 55 | 56 | [ angles ] 57 | ; ai aj ak funct c0 c1 c2 c3 58 | 2 1 6 5 59 | 1 2 3 5 60 | 1 2 7 5 61 | 3 2 7 5 62 | 2 3 4 5 63 | 2 3 8 5 64 | 4 3 8 5 65 | 9 4 3 5 66 | 9 4 5 5 67 | 3 4 5 5 68 | 10 5 4 5 69 | 10 5 6 5 70 | 4 5 6 5 71 | 1 6 11 5 72 | 1 6 5 5 73 | 11 6 5 5 74 | 75 | [ dihedrals ] 76 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 77 | 6 1 2 3 9 78 | 6 1 2 7 9 79 | 2 1 6 11 9 80 | 2 1 6 5 9 81 | 1 2 3 4 9 82 | 1 2 3 8 9 83 | 7 2 3 4 9 84 | 7 2 3 8 9 85 | 2 3 4 9 9 86 | 2 3 4 5 9 87 | 8 3 4 9 9 88 | 8 3 4 5 9 89 | 9 4 5 10 9 90 | 9 4 5 6 9 91 | 3 4 5 10 9 92 | 3 4 5 6 9 93 | 10 5 6 1 9 94 | 10 5 6 11 9 95 | 4 5 6 1 9 96 | 4 5 6 11 9 97 | 98 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/pyr1.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 9/10/12 11:30:23 CREATED BY USER: prabhu 3 | ATOM 1 N1 PYR1 1 0.005 0.064 -0.000 1.00 0.00 PYR1 4 | ATOM 2 C2 PYR1 1 1.335 -0.012 0.000 1.00 0.00 PYR1 5 | ATOM 3 C3 PYR1 1 2.144 1.136 0.000 1.00 0.00 PYR1 6 | ATOM 4 C4 PYR1 1 1.518 2.393 0.000 1.00 0.00 PYR1 7 | ATOM 5 C5 PYR1 1 0.115 2.454 0.000 1.00 0.00 PYR1 8 | ATOM 6 C6 PYR1 1 -0.605 1.248 -0.000 1.00 0.00 PYR1 9 | ATOM 7 H2 PYR1 1 1.782 -0.998 0.000 1.00 0.00 PYR1 10 | ATOM 8 H3 PYR1 1 3.218 1.048 0.000 1.00 0.00 PYR1 11 | ATOM 9 H4 PYR1 1 2.106 3.299 0.000 1.00 0.00 PYR1 12 | ATOM 10 H5 PYR1 1 -0.402 3.400 0.000 1.00 0.00 PYR1 13 | ATOM 11 H6 PYR1 1 -1.688 1.257 -0.000 1.00 0.00 PYR1 14 | TER 12 PYR1 1 15 | END 16 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/sol.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 11/ 3/11 18: 5:14 CREATED BY USER: prabhu 3 | ATOM 1 OW SOL 1 0.000 -0.391 0.000 1.00 0.00 SOL 4 | ATOM 2 HW1 SOL 1 0.757 0.195 0.000 1.00 0.00 SOL 5 | ATOM 3 HW2 SOL 1 -0.757 0.195 0.000 1.00 0.00 SOL 6 | TER 4 SOL 1 7 | END 8 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/tolu.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'tolu.top' was generated 3 | ; By user: onbekend (0) 4 | ; On host: onbekend 5 | ; At date: Fri May 4 17:46:43 2012 6 | ; 7 | ; This is a standalone topology file 8 | ; 9 | ; It was generated using program: 10 | ; pdb2gmx - VERSION 4.5.4 11 | ; 12 | ; Command line was: 13 | ; pdb2gmx -f tolu.pdb -p tolu.top -ff gd-charmm27 -water tip3p 14 | ; 15 | ; Force field was read from current directory or a relative path - path added. 16 | ; 17 | 18 | [ moleculetype ] 19 | ; Name nrexcl 20 | TOLU 3 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 24 | ; residue 1 TOLU rtp TOLU q 0.0 25 | 1 CG2R61 1 TOLU CG 1 -0.115 12.011 ; qtot -0.115 26 | 2 HGR61 1 TOLU HG 2 0.115 1.008 ; qtot 0 27 | 3 CG2R61 1 TOLU CD1 3 -0.115 12.011 ; qtot -0.115 28 | 4 HGR61 1 TOLU HD1 4 0.115 1.008 ; qtot 0 29 | 5 CG2R61 1 TOLU CD2 5 -0.115 12.011 ; qtot -0.115 30 | 6 HGR61 1 TOLU HD2 6 0.115 1.008 ; qtot 0 31 | 7 CG2R61 1 TOLU CE1 7 -0.115 12.011 ; qtot -0.115 32 | 8 HGR61 1 TOLU HE1 8 0.115 1.008 ; qtot 0 33 | 9 CG2R61 1 TOLU CE2 9 -0.115 12.011 ; qtot -0.115 34 | 10 HGR61 1 TOLU HE2 10 0.115 1.008 ; qtot 0 35 | 11 CG2R61 1 TOLU CZ 11 0 12.011 ; qtot 0 36 | 12 CG331 1 TOLU CT 12 -0.27 12.011 ; qtot -0.27 37 | 13 HGA3 1 TOLU H11 13 0.09 1.008 ; qtot -0.18 38 | 14 HGA3 1 TOLU H12 14 0.09 1.008 ; qtot -0.09 39 | 15 HGA3 1 TOLU H13 15 0.09 1.008 ; qtot 0 40 | 41 | [ bonds ] 42 | ; ai aj funct c0 c1 c2 c3 43 | 1 2 1 44 | 1 3 1 45 | 1 5 1 46 | 3 4 1 47 | 3 7 1 48 | 5 6 1 49 | 5 9 1 50 | 7 8 1 51 | 7 11 1 52 | 9 10 1 53 | 9 11 1 54 | 11 12 1 55 | 12 13 1 56 | 12 14 1 57 | 12 15 1 58 | 59 | [ pairs ] 60 | ; ai aj funct c0 c1 c2 c3 61 | 1 8 1 62 | 1 10 1 63 | 1 11 1 64 | 2 4 1 65 | 2 6 1 66 | 2 7 1 67 | 2 9 1 68 | 3 6 1 69 | 3 9 1 70 | 3 12 1 71 | 4 5 1 72 | 4 8 1 73 | 4 11 1 74 | 5 7 1 75 | 5 12 1 76 | 6 10 1 77 | 6 11 1 78 | 7 10 1 79 | 7 13 1 80 | 7 14 1 81 | 7 15 1 82 | 8 9 1 83 | 8 12 1 84 | 9 13 1 85 | 9 14 1 86 | 9 15 1 87 | 10 12 1 88 | 89 | [ angles ] 90 | ; ai aj ak funct c0 c1 c2 c3 91 | 2 1 3 5 92 | 2 1 5 5 93 | 3 1 5 5 94 | 1 3 4 5 95 | 1 3 7 5 96 | 4 3 7 5 97 | 1 5 6 5 98 | 1 5 9 5 99 | 6 5 9 5 100 | 3 7 8 5 101 | 3 7 11 5 102 | 8 7 11 5 103 | 5 9 10 5 104 | 5 9 11 5 105 | 10 9 11 5 106 | 7 11 9 5 107 | 7 11 12 5 108 | 9 11 12 5 109 | 11 12 13 5 110 | 11 12 14 5 111 | 11 12 15 5 112 | 13 12 14 5 113 | 13 12 15 5 114 | 14 12 15 5 115 | 116 | [ dihedrals ] 117 | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 118 | 2 1 3 4 9 119 | 2 1 3 7 9 120 | 5 1 3 4 9 121 | 5 1 3 7 9 122 | 2 1 5 6 9 123 | 2 1 5 9 9 124 | 3 1 5 6 9 125 | 3 1 5 9 9 126 | 1 3 7 8 9 127 | 1 3 7 11 9 128 | 4 3 7 8 9 129 | 4 3 7 11 9 130 | 1 5 9 10 9 131 | 1 5 9 11 9 132 | 6 5 9 10 9 133 | 6 5 9 11 9 134 | 3 7 11 9 9 135 | 3 7 11 12 9 136 | 8 7 11 9 9 137 | 8 7 11 12 9 138 | 5 9 11 7 9 139 | 5 9 11 12 9 140 | 10 9 11 7 9 141 | 10 9 11 12 9 142 | 7 11 12 13 9 143 | 7 11 12 14 9 144 | 7 11 12 15 9 145 | 9 11 12 13 9 146 | 9 11 12 14 9 147 | 9 11 12 15 9 148 | 149 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/mol/tolu.pdb: -------------------------------------------------------------------------------- 1 | REMARK FOO 2 | REMARK DATE: 5/ 4/12 17:43:49 CREATED BY USER: prabhu 3 | ATOM 1 CG TOLU 1 -0.001 -0.002 -0.002 1.00 0.00 TOLU 4 | ATOM 2 HG TOLU 1 -0.541 -0.938 -0.005 1.00 0.00 TOLU 5 | ATOM 3 CD1 TOLU 1 1.400 -0.002 -0.000 1.00 0.00 TOLU 6 | ATOM 4 HD1 TOLU 1 1.941 -0.938 -0.004 1.00 0.00 TOLU 7 | ATOM 5 CD2 TOLU 1 -0.702 1.212 -0.000 1.00 0.00 TOLU 8 | ATOM 6 HD2 TOLU 1 -1.782 1.212 -0.004 1.00 0.00 TOLU 9 | ATOM 7 CE1 TOLU 1 2.100 1.212 0.003 1.00 0.00 TOLU 10 | ATOM 8 HE1 TOLU 1 3.180 1.214 0.002 1.00 0.00 TOLU 11 | ATOM 9 CE2 TOLU 1 -0.000 2.425 0.003 1.00 0.00 TOLU 12 | ATOM 10 HE2 TOLU 1 -0.538 3.361 0.002 1.00 0.00 TOLU 13 | ATOM 11 CZ TOLU 1 1.403 2.430 0.010 1.00 0.00 TOLU 14 | ATOM 12 CT TOLU 1 2.151 3.726 0.002 1.00 0.00 TOLU 15 | ATOM 13 H11 TOLU 1 2.326 4.029 -1.053 1.00 0.00 TOLU 16 | ATOM 14 H12 TOLU 1 3.124 3.599 0.524 1.00 0.00 TOLU 17 | ATOM 15 H13 TOLU 1 1.555 4.505 0.524 1.00 0.00 TOLU 18 | TER 16 TOLU 1 19 | END 20 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/nbfix.itp: -------------------------------------------------------------------------------- 1 | ; NBFIX rmin=/2^(1/6), eps=4.184* 2 | ;name type1 type2 1 sigma epsilon 3 | [ nonbond_params ] 4 | NC2 OC 1 0.324019863788 0.648181096000 5 | SOD CLA 1 0.332394311738 0.350933000000 6 | POT CLA 1 0.363575766873 0.477963424000 7 | SOD OCL 1 0.287760285959 0.313883680000 8 | SOD OBL 1 0.278851298778 0.313883680000 9 | SOD O2L 1 0.281523994932 0.313883680000 10 | SOD OC 1 0.287760285959 0.313883680000 11 | SOD OC2D2 1 0.287760285959 0.313883680000 12 | SOD OG2D2 1 0.287760285959 0.313883680000 13 | OG2D1 CLGR1 1 0.302905564168 0.836800000000 14 | O CLGR1 1 0.302905564168 0.836800000000 15 | ON1 CLGR1 1 0.302905564168 0.836800000000 16 | ON1C CLGR1 1 0.302905564168 0.836800000000 17 | OC2D1 CLGR1 1 0.302905564168 0.836800000000 18 | CRL1 HAL2 1 0.298451070577 0.134306400000 19 | HGA1 HAL2 1 0.238760856462 0.150205600000 20 | CRL2 HAL2 1 0.299341969295 0.173636000000 21 | HGA2 HAL2 1 0.238760856462 0.132632800000 22 | CRL1 HAL1 1 0.298451070577 0.122591200000 23 | HGA1 HAL1 1 0.238760856462 0.137653600000 24 | CRL2 HAL1 1 0.299341969295 0.158573600000 25 | HGA2 HAL1 1 0.238760856462 0.120917600000 26 | CRL1 CTL1 1 0.357250385974 0.115060000000 27 | HGA1 CTL1 1 0.297560171859 0.128867200000 28 | CRL2 CTL1 1 0.358141284692 0.148532000000 29 | HGA2 CTL1 1 0.297560171859 0.113386400000 30 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/silcs.itp: -------------------------------------------------------------------------------- 1 | ; for SILCS, pram 2 | 3 | [ atomtypes ] 4 | ;type atnum mass charge ? sigma epsilon 5 | ; special dummy-type particles 6 | LP 0 0.000000 0.00 A 0.0 0.0 ; pram 7 | LQ 0 0.000000 0.00 A 0.0 0.0 ; pram 8 | 9 | ; NBFIX for LP, rmin=1.2/2^(1/6), eps=4.184*.01 10 | [ nonbond_params ] 11 | LP LP 1 1.069078461768 0.041840000000 ; pram 12 | LQ LQ 1 1.069078461768 0.041840000000 ; pram 13 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/spc.itp: -------------------------------------------------------------------------------- 1 | 2 | [ moleculetype ] 3 | ; molname nrexcl 4 | SOL 2 5 | 6 | [ atoms ] 7 | ; nr type resnr residue atom cgnr charge mass 8 | 1 OW 1 SOL OW 1 -0.82 9 | 2 HW 1 SOL HW1 1 0.41 10 | 3 HW 1 SOL HW2 1 0.41 11 | 12 | #ifndef FLEXIBLE 13 | [ settles ] 14 | ; OW funct doh dhh 15 | 1 1 0.1 0.16330 16 | 17 | [ exclusions ] 18 | 1 2 3 19 | 2 1 3 20 | 3 1 2 21 | #else 22 | [ bonds ] 23 | ; i j funct length force.c. 24 | 1 2 1 0.1 345000 0.1 345000 25 | 1 3 1 0.1 345000 0.1 345000 26 | 27 | [ angles ] 28 | ; i j k funct angle force.c. 29 | 2 1 3 1 109.47 383 109.47 383 30 | #endif 31 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/spce.itp: -------------------------------------------------------------------------------- 1 | 2 | [ moleculetype ] 3 | ; molname nrexcl 4 | SOL 2 5 | 6 | [ atoms ] 7 | ; nr type resnr residue atom cgnr charge mass 8 | 1 OW 1 SOL OW 1 -0.8476 9 | 2 HW 1 SOL HW1 1 0.4238 10 | 3 HW 1 SOL HW2 1 0.4238 11 | 12 | #ifndef FLEXIBLE 13 | [ settles ] 14 | ; OW funct doh dhh 15 | 1 1 0.1 0.16330 16 | 17 | [ exclusions ] 18 | 1 2 3 19 | 2 1 3 20 | 3 1 2 21 | #else 22 | [ bonds ] 23 | ; i j funct length force.c. 24 | 1 2 1 0.1 345000 0.1 345000 25 | 1 3 1 0.1 345000 0.1 345000 26 | 27 | [ angles ] 28 | ; i j k funct angle force.c. 29 | 2 1 3 1 109.47 383 109.47 383 30 | #endif 31 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/tip3p.itp: -------------------------------------------------------------------------------- 1 | 2 | [ moleculetype ] 3 | ; molname nrexcl 4 | SOL 2 5 | 6 | [ atoms ] 7 | ; id at type res nr residu name at name cg nr charge 8 | #ifdef _FF_CHARMM 9 | 1 OT 1 SOL OW 1 -0.834 10 | 2 HT 1 SOL HW1 1 0.417 11 | 3 HT 1 SOL HW2 1 0.417 12 | #endif 13 | 14 | 15 | #ifdef FLEXIBLE 16 | 17 | #ifdef ORIGINAL_TIP3P 18 | [ bonds ] 19 | ; i j funct length force.c. 20 | 1 2 1 0.09572 502416.0 0.09572 502416.0 21 | 1 3 1 0.09572 502416.0 0.09572 502416.0 22 | 23 | [ angles ] 24 | ; i j k funct angle force.c. 25 | 2 1 3 1 104.52 628.02 104.52 628.02 26 | 27 | #else 28 | ;CHARMM TIP3p 29 | [ bonds ] 30 | ; i j funct length force.c. 31 | 1 2 1 0.09572 376560.0 0.09572 376560.0 32 | 1 3 1 0.09572 376560.0 0.09572 376560.0 33 | 34 | [ angles ] 35 | ; i j k funct angle force.c. 36 | 2 1 3 1 104.52 460.24 104.52 460.24 37 | #endif 38 | 39 | 40 | #else 41 | [ settles ] 42 | ; i j funct length 43 | 1 1 0.09572 0.15139 44 | 45 | [ exclusions ] 46 | 1 2 3 47 | 2 1 3 48 | 3 1 2 49 | #endif 50 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/tip4p.itp: -------------------------------------------------------------------------------- 1 | 2 | ; 3 | ; Note the strange order of atoms to make it faster in gromacs. 4 | ; 5 | [ moleculetype ] 6 | ; molname nrexcl 7 | SOL 2 8 | 9 | [ atoms ] 10 | ; id at type res nr residu name at name cg nr charge 11 | 1 OWT4 1 SOL OW 1 0.0 12 | 2 HWT4 1 SOL HW1 1 0.52 13 | 3 HWT4 1 SOL HW2 1 0.52 14 | 4 MWT4 1 SOL MW 1 -1.04 15 | 16 | #ifndef FLEXIBLE 17 | [ settles ] 18 | ; OW funct doh dhh 19 | 1 1 0.09572 0.15139 20 | #else 21 | [ bonds ] 22 | ; i j funct length force.c. 23 | 1 2 1 0.09572 502416.0 0.09572 502416.0 24 | 1 3 1 0.09572 502416.0 0.09572 502416.0 25 | 26 | [ angles ] 27 | ; i j k funct angle force.c. 28 | 2 1 3 1 104.52 628.02 104.52 628.02 29 | #endif 30 | 31 | [ exclusions ] 32 | 1 2 3 4 33 | 2 1 3 4 34 | 3 1 2 4 35 | 4 1 2 3 36 | 37 | ; The position of the virtual site is computed as follows: 38 | ; 39 | ; O 40 | ; 41 | ; D 42 | ; 43 | ; H H 44 | ; 45 | ; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ] 46 | ; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ] 47 | 48 | ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) 49 | 50 | [ virtual_sites3 ] 51 | ; Vsite from funct a b 52 | 4 1 2 3 1 0.128012065 0.128012065 53 | 54 | -------------------------------------------------------------------------------- /examples/CGenFF/charmm36.ff/watermodels.dat: -------------------------------------------------------------------------------- 1 | 2 | tip3p TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H 3 | tip4p TIP4P TIP 4-point 4 | tip5p TIP5P TIP 5-point 5 | spc SPC simple point charge 6 | spce SPC/E extended simple point charge 7 | -------------------------------------------------------------------------------- /examples/CGenFF/quinoline/LIG_ffbonded.itp: -------------------------------------------------------------------------------- 1 | ; This force field generated by mol2tortp for ligand specific params 2 | ; Copyright University of Maryland, School of Pharmacy 3 | 4 | -------------------------------------------------------------------------------- /examples/CGenFF/quinoline/after_cg.g96: -------------------------------------------------------------------------------- 1 | TITLE 2 | Ligand 3 | END 4 | POSITION 5 | 1 LIG C1 1 1.990131328 2.083434900 2.000000000 6 | 1 LIG C2 2 2.111820467 2.152635918 2.000000000 7 | 1 LIG H3 3 2.110652112 2.260587095 2.000000000 8 | 1 LIG C4 4 2.233652284 2.083195255 2.000000000 9 | 1 LIG H5 5 2.326915930 2.137857658 2.000000000 10 | 1 LIG C6 6 2.234457450 1.943111177 2.000000000 11 | 1 LIG H7 7 2.328578943 1.889917187 2.000000000 12 | 1 LIG C8 8 2.113898559 1.871563336 2.000000000 13 | 1 LIG H9 9 2.116036377 1.763482029 2.000000000 14 | 1 LIG C10 10 1.991899501 1.940441246 2.000000000 15 | 1 LIG C11 11 1.868720144 1.873084382 2.000000000 16 | 1 LIG H12 12 1.864456307 1.765137021 2.000000000 17 | 1 LIG C13 13 1.749966589 1.948001481 2.000000000 18 | 1 LIG H14 14 1.653679807 1.899479913 2.000000000 19 | 1 LIG C15 15 1.758754784 2.088065042 2.000000000 20 | 1 LIG H16 16 1.668718979 2.148402284 2.000000000 21 | 1 LIG N17 17 1.875660439 2.151604074 2.000000000 22 | END 23 | BOX 24 | 4.000000000 4.000000000 4.000000000 25 | END 26 | -------------------------------------------------------------------------------- /examples/CGenFF/quinoline/cg.tpr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/CGenFF/quinoline/cg.tpr -------------------------------------------------------------------------------- /examples/CGenFF/quinoline/conf.gro: -------------------------------------------------------------------------------- 1 | Good gRace! Old Maple Actually Chews Slate 2 | 17 3 | 1LIG C1 1 1.990 2.083 2.000 4 | 1LIG C2 2 2.113 2.152 2.000 5 | 1LIG H3 3 2.110 2.260 2.000 6 | 1LIG C4 4 2.232 2.084 2.000 7 | 1LIG H5 5 2.326 2.138 2.000 8 | 1LIG C6 6 2.233 1.942 2.000 9 | 1LIG H7 7 2.328 1.890 2.000 10 | 1LIG C8 8 2.116 1.872 2.000 11 | 1LIG H9 9 2.116 1.764 2.000 12 | 1LIG C10 10 1.992 1.940 2.000 13 | 1LIG C11 11 1.867 1.873 2.000 14 | 1LIG H12 12 1.864 1.765 2.000 15 | 1LIG C13 13 1.752 1.947 2.000 16 | 1LIG H14 14 1.654 1.900 2.000 17 | 1LIG C15 15 1.761 2.088 2.000 18 | 1LIG H16 16 1.670 2.148 2.000 19 | 1LIG N17 17 1.874 2.154 2.000 20 | 4.00000 4.00000 4.00000 21 | -------------------------------------------------------------------------------- /examples/CGenFF/quinoline/eigenfreq.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Wed Jun 19 21:30:20 2019 2 | # Created by: 3 | # :-) GROMACS - gmx nmeig, 2019.2-dev-20190326-dfd7b5ac4-dirty (double precision) (-: 4 | # 5 | # Executable: /Users/spoel/software-release-2019/bin/gmx_mpi_d 6 | # Data prefix: /Users/spoel/software-release-2019 7 | # Working dir: /Users/spoel/Liquids/FORCE_FIELD/THERMO/CGenFF/quinoline 8 | # Command line: 9 | # gmx_mpi_d nmeig -last 1000 -s nm.tpr -f nm.mtx -sigma 1 10 | # gmx nmeig is part of G R O M A C S: 11 | # 12 | # Giant Rising Ordinary Mutants for A Clerical Setup 13 | # 14 | @ title "Eigenfrequencies" 15 | @ xaxis label "Eigenvector index" 16 | @ yaxis label "Wavenumber [cm\S-1\N]" 17 | @TYPE xy 18 | @ subtitle "mass weighted" 19 | 1 0 20 | 2 0 21 | 3 0 22 | 4 0 23 | 5 0.00359433 24 | 6 0.0132784 25 | 7 166.588 26 | 8 195.759 27 | 9 356.901 28 | 10 358.619 29 | 11 433.906 30 | 12 462.637 31 | 13 473.787 32 | 14 540.555 33 | 15 550.418 34 | 16 636.777 35 | 17 725.885 36 | 18 753.14 37 | 19 769.266 38 | 20 793.387 39 | 21 796.309 40 | 22 861.461 41 | 23 905.035 42 | 24 934.207 43 | 25 986.229 44 | 26 988.42 45 | 27 997.58 46 | 28 1007.7 47 | 29 1043.19 48 | 30 1062.94 49 | 31 1109.02 50 | 32 1196.86 51 | 33 1220.87 52 | 34 1248.52 53 | 35 1283.56 54 | 36 1378.07 55 | 37 1430.24 56 | 38 1431.53 57 | 39 1438.69 58 | 40 1467.56 59 | 41 1487.6 60 | 42 1515.81 61 | 43 1531.55 62 | 44 1620.92 63 | 45 3055.29 64 | 46 3055.44 65 | 47 3056.02 66 | 48 3057.27 67 | 49 3058.58 68 | 50 3060.68 69 | 51 3085.4 70 | -------------------------------------------------------------------------------- /examples/CGenFF/quinoline/eigenval.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Wed Jun 19 21:30:20 2019 2 | # Created by: 3 | # :-) GROMACS - gmx nmeig, 2019.2-dev-20190326-dfd7b5ac4-dirty (double precision) (-: 4 | # 5 | # Executable: /Users/spoel/software-release-2019/bin/gmx_mpi_d 6 | # Data prefix: /Users/spoel/software-release-2019 7 | # Working dir: /Users/spoel/Liquids/FORCE_FIELD/THERMO/CGenFF/quinoline 8 | # Command line: 9 | # gmx_mpi_d nmeig -last 1000 -s nm.tpr -f nm.mtx -sigma 1 10 | # gmx nmeig is part of G R O M A C S: 11 | # 12 | # GROningen Mixture of Alchemy and Childrens' Stories 13 | # 14 | @ title "Eigenvalues" 15 | @ xaxis label "Eigenvalue index" 16 | @ yaxis label "Eigenvalue [Gromacs units]" 17 | @TYPE xy 18 | @ subtitle "mass weighted" 19 | 1 -2.00974e-05 20 | 2 -6.08357e-06 21 | 3 -1.91994e-07 22 | 4 -4.78676e-08 23 | 5 4.58393e-07 24 | 6 6.25591e-06 25 | 7 984.661 26 | 8 1359.7 27 | 9 4519.57 28 | 10 4563.19 29 | 11 6680.25 30 | 12 7594.21 31 | 13 7964.65 32 | 14 10367.7 33 | 15 10749.4 34 | 16 14387.2 35 | 17 18695.5 36 | 18 20125.7 37 | 19 20996.8 38 | 20 22334.3 39 | 21 22499.1 40 | 22 26331.3 41 | 23 29062.4 42 | 24 30966.2 43 | 25 34510.9 44 | 26 34664.4 45 | 27 35309.9 46 | 28 36030.1 47 | 29 38612.4 48 | 30 40088.3 49 | 31 43639.5 50 | 32 50825.9 51 | 33 52886.1 52 | 34 55308.5 53 | 35 58456.4 54 | 36 67382.1 55 | 37 72580.8 56 | 38 72711.3 57 | 39 73440.8 58 | 40 76417.2 59 | 41 78519.1 60 | 42 81525.4 61 | 43 83226.9 62 | 44 93223.3 63 | 45 331212 64 | 46 331245 65 | 47 331370 66 | 48 331642 67 | 49 331927 68 | 50 332382 69 | 51 337772 70 | -------------------------------------------------------------------------------- /examples/CGenFF/quinoline/eigenvec.trr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/CGenFF/quinoline/eigenvec.trr -------------------------------------------------------------------------------- /examples/CGenFF/quinoline/ener.edr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/CGenFF/quinoline/ener.edr -------------------------------------------------------------------------------- /examples/CGenFF/quinoline/minimize.tpr: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | TITLE 2 | MOL 3 | END 4 | POSITION 5 | 1 MOL C1 1 2.172123962 1.921792461 1.995813345 6 | 1 MOL H1 2 2.195618505 1.932670482 1.889633849 7 | 1 MOL H2 3 2.140998848 1.819332805 2.018102320 8 | 1 MOL H3 4 1.848026145 2.179273506 2.001494132 9 | 1 MOL C2 5 2.063677396 2.018397345 2.033301646 10 | 1 MOL O1 6 2.083223198 2.110362605 2.109499422 11 | 1 MOL N1 7 1.943121857 1.992389182 1.973591498 12 | 1 MOL H4 8 1.750199305 2.056130798 1.916129947 13 | 1 MOL C3 9 1.822248813 2.072524328 1.997234304 14 | 1 MOL H5 10 1.776610298 2.043162719 2.092637741 15 | 1 MOL H6 11 1.939368040 1.912431036 1.912434585 16 | 1 MOL H7 12 2.260783634 1.946532733 2.055127211 17 | END 18 | BOX 19 | 4.000000000 4.000000000 4.000000000 20 | END 21 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/N-methylacetamide/conf.gro: -------------------------------------------------------------------------------- 1 | MOL_GMX.gro created by acpype (Rev: 0) on Wed Feb 14 17:48:29 2018 2 | 12 3 | 1MOL C1 1 2.174 1.923 1.993 4 | 1MOL H1 2 2.242 1.958 1.915 5 | 1MOL H2 3 2.136 1.825 1.965 6 | 1MOL H3 4 1.856 2.168 2.032 7 | 1MOL C2 5 2.065 2.027 2.011 8 | 1MOL O1 6 2.091 2.142 2.042 9 | 1MOL N1 7 1.937 1.983 1.991 10 | 1MOL H4 8 1.766 2.076 1.910 11 | 1MOL C3 9 1.821 2.069 2.004 12 | 1MOL H5 10 1.754 2.032 2.082 13 | 1MOL H6 11 1.924 1.887 1.965 14 | 1MOL H7 12 2.230 1.915 2.085 15 | 4.00000 4.00000 4.00000 16 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/N-methylacetamide/eigenfreq.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Oct 7 19:53:48 2018 2 | # Created by: 3 | # :-) GROMACS - gmx nmeig, 2019-dev-20181004-83c2c3a2f (double precision) (-: 4 | # 5 | # Executable: /Users/spoel/software-master/bin/gmx_mpi_d 6 | # Data prefix: /Users/spoel/software-master 7 | # Working dir: /Users/spoel/Liquids/FORCE_FIELD/THERMO/GAFF-ESP/N-methylacetamide 8 | # Command line: 9 | # gmx_mpi_d nmeig -maxspec 5000 -s nm -f nm.mtx -sigma 1 -last 500 -scale 1.018000 10 | # gmx nmeig is part of G R O M A C S: 11 | # 12 | # GROtesk MACabre and Sinister 13 | # 14 | @ title "Eigenfrequencies" 15 | @ xaxis label "Eigenvector index" 16 | @ yaxis label "Wavenumber [cm\S-1\N]" 17 | @TYPE xy 18 | @ subtitle "mass weighted" 19 | 1 0 20 | 2 0 21 | 3 0 22 | 4 0 23 | 5 0.00352836 24 | 6 0.0280532 25 | 7 67.0645 26 | 8 110.512 27 | 9 138.339 28 | 10 295.273 29 | 11 421.442 30 | 12 575.382 31 | 13 580.951 32 | 14 649.496 33 | 15 798.477 34 | 16 951.004 35 | 17 999.829 36 | 18 1030.27 37 | 19 1047.22 38 | 20 1083.25 39 | 21 1274.22 40 | 22 1459.83 41 | 23 1465.31 42 | 24 1468.13 43 | 25 1478.14 44 | 26 1484.37 45 | 27 1510.19 46 | 28 1695.35 47 | 29 1709.01 48 | 30 2826.99 49 | 31 2828.81 50 | 32 2939.16 51 | 33 2940.6 52 | 34 2941.23 53 | 35 2942.16 54 | 36 3186.11 55 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/N-methylacetamide/eigenval.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Oct 7 19:53:48 2018 2 | # Created by: 3 | # :-) GROMACS - gmx nmeig, 2019-dev-20181004-83c2c3a2f (double precision) (-: 4 | # 5 | # Executable: /Users/spoel/software-master/bin/gmx_mpi_d 6 | # Data prefix: /Users/spoel/software-master 7 | # Working dir: /Users/spoel/Liquids/FORCE_FIELD/THERMO/GAFF-ESP/N-methylacetamide 8 | # Command line: 9 | # gmx_mpi_d nmeig -maxspec 5000 -s nm -f nm.mtx -sigma 1 -last 500 -scale 1.018000 10 | # gmx nmeig is part of G R O M A C S: 11 | # 12 | # Gyas ROwers Mature At Cryogenic Speed 13 | # 14 | @ title "Eigenvalues" 15 | @ xaxis label "Eigenvalue index" 16 | @ yaxis label "Eigenvalue [Gromacs units]" 17 | @TYPE xy 18 | @ subtitle "mass weighted" 19 | 1 -2.78786e-05 20 | 2 -2.03009e-05 21 | 3 -3.65168e-07 22 | 4 -1.25748e-07 23 | 5 4.4172e-07 24 | 6 2.79232e-05 25 | 7 159.583 26 | 8 433.329 27 | 9 679.03 28 | 10 3093.49 29 | 11 6301.98 30 | 12 11746.7 31 | 13 11975.1 32 | 14 14967.7 33 | 15 22621.7 34 | 16 32089.7 35 | 17 35469.3 36 | 18 37661.9 37 | 19 38911.2 38 | 20 41635.3 39 | 21 57608.6 40 | 22 75614.1 41 | 23 76183.6 42 | 24 76477.1 43 | 25 77523.3 44 | 26 78178 45 | 27 80921.6 46 | 28 101981 47 | 29 103631 48 | 30 283562 49 | 31 283928 50 | 32 306513 51 | 33 306812 52 | 34 306944 53 | 35 307138 54 | 36 360182 55 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/N-methylacetamide/eigenvec.trr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/GAFF-ESP/N-methylacetamide/eigenvec.trr -------------------------------------------------------------------------------- /examples/GAFF-ESP/N-methylacetamide/ener.edr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/GAFF-ESP/N-methylacetamide/ener.edr -------------------------------------------------------------------------------- /examples/GAFF-ESP/N-methylacetamide/minimize.tpr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/GAFF-ESP/N-methylacetamide/minimize.tpr -------------------------------------------------------------------------------- /examples/GAFF-ESP/N-methylacetamide/nm.mtx: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | TITLE 2 | MOL 3 | END 4 | POSITION 5 | 1 MOL O1 1 2.000000000 2.000000000 2.058620000 6 | 1 MOL C1 2 2.000000000 2.000000000 1.941380000 7 | END 8 | BOX 9 | 4.000000000 4.000000000 4.000000000 10 | END 11 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/carbon-monoxide/carbon-monoxide-3-oep.log.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/GAFF-ESP/carbon-monoxide/carbon-monoxide-3-oep.log.gz -------------------------------------------------------------------------------- /examples/GAFF-ESP/carbon-monoxide/carbon-monoxide-g4.log.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/GAFF-ESP/carbon-monoxide/carbon-monoxide-g4.log.gz -------------------------------------------------------------------------------- /examples/GAFF-ESP/carbon-monoxide/conf.gro: -------------------------------------------------------------------------------- 1 | MOL_GMX.gro created by acpype (Rev: 0) on Wed Feb 14 17:43:35 2018 2 | 2 3 | 1MOL O1 1 2.000 2.000 2.056 4 | 1MOL C1 2 2.000 2.000 1.944 5 | 4.00000 4.00000 4.00000 6 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/carbon-monoxide/eigenfreq.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Oct 7 20:01:13 2018 2 | # Created by: 3 | # :-) GROMACS - gmx nmeig, 2019-dev-20181004-83c2c3a2f (double precision) (-: 4 | # 5 | # Executable: /Users/spoel/software-master/bin/gmx_mpi_d 6 | # Data prefix: /Users/spoel/software-master 7 | # Working dir: /Users/spoel/Liquids/FORCE_FIELD/THERMO/GAFF-ESP/carbon-monoxide 8 | # Command line: 9 | # gmx_mpi_d nmeig -maxspec 5000 -s nm -f nm.mtx -sigma 1 -last 500 -scale 1.018000 10 | # gmx nmeig is part of G R O M A C S: 11 | # 12 | # Great Red Owns Many ACres of Sand 13 | # 14 | @ title "Eigenfrequencies" 15 | @ xaxis label "Eigenvector index" 16 | @ yaxis label "Wavenumber [cm\S-1\N]" 17 | @TYPE xy 18 | @ subtitle "mass weighted" 19 | 1 0 20 | 2 3.34519e-11 21 | 3 3.50768e-05 22 | 4 0.00144931 23 | 5 0.00144932 24 | 6 1614.36 25 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/carbon-monoxide/eigenval.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Oct 7 20:01:12 2018 2 | # Created by: 3 | # :-) GROMACS - gmx nmeig, 2019-dev-20181004-83c2c3a2f (double precision) (-: 4 | # 5 | # Executable: /Users/spoel/software-master/bin/gmx_mpi_d 6 | # Data prefix: /Users/spoel/software-master 7 | # Working dir: /Users/spoel/Liquids/FORCE_FIELD/THERMO/GAFF-ESP/carbon-monoxide 8 | # Command line: 9 | # gmx_mpi_d nmeig -maxspec 5000 -s nm -f nm.mtx -sigma 1 -last 500 -scale 1.018000 10 | # gmx nmeig is part of G R O M A C S: 11 | # 12 | # God Rules Over Mankind, Animals, Cosmos and Such 13 | # 14 | @ title "Eigenvalues" 15 | @ xaxis label "Eigenvalue index" 16 | @ yaxis label "Eigenvalue [Gromacs units]" 17 | @TYPE xy 18 | @ subtitle "mass weighted" 19 | 1 -7.88478e-13 20 | 2 3.97047e-23 21 | 3 4.36557e-11 22 | 4 7.45284e-08 23 | 5 7.45294e-08 24 | 6 92469.7 25 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/carbon-monoxide/eigenvec.trr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/GAFF-ESP/carbon-monoxide/eigenvec.trr -------------------------------------------------------------------------------- /examples/GAFF-ESP/carbon-monoxide/ener.edr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/GAFF-ESP/carbon-monoxide/ener.edr -------------------------------------------------------------------------------- /examples/GAFF-ESP/carbon-monoxide/minimize.tpr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/GAFF-ESP/carbon-monoxide/minimize.tpr -------------------------------------------------------------------------------- /examples/GAFF-ESP/carbon-monoxide/nm.mtx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/GAFF-ESP/carbon-monoxide/nm.mtx -------------------------------------------------------------------------------- /examples/GAFF-ESP/carbon-monoxide/nm.tpr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/GAFF-ESP/carbon-monoxide/nm.tpr -------------------------------------------------------------------------------- /examples/GAFF-ESP/carbon-monoxide/old.top: -------------------------------------------------------------------------------- 1 | ; Topology generated from /home/ghahremanpour/Liquids/MOLECULES/OEP/carbon-monoxide/carbon-monoxide-3-oep.log.gz 2 | ; Charge method used esp 3 | ; MOL_GMX.top created by acpype (Rev: 0) on Wed Feb 14 17:43:35 2018 4 | 5 | [ defaults ] 6 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 7 | 1 2 yes 0.5 0.8333 8 | 9 | [ atomtypes ] 10 | ;name bond_type mass charge ptype sigma epsilon Amb 11 | o o 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 12 | c1 c1 0.00000 0.00000 A 3.39967e-01 8.78640e-01 ; 1.91 0.2100 13 | 14 | [ moleculetype ] 15 | ;name nrexcl 16 | MOL 3 17 | 18 | [ atoms ] 19 | ; nr type resi res atom cgnr charge mass ; qtot bond_type 20 | 1 o 1 MOL O1 1 0.006571 16.00000 ; qtot 0.007 21 | 2 c1 1 MOL C1 2 -0.006571 12.01000 ; qtot 0.000 22 | 23 | [ bonds ] 24 | ; ai aj funct r k 25 | 1 2 1 1.1724e-01 6.3438e+05 ; O1 - C1 26 | 27 | [ system ] 28 | MOL 29 | 30 | [ molecules ] 31 | ; Compound nmols 32 | MOL 1 33 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/carbon-monoxide/topol.top: -------------------------------------------------------------------------------- 1 | ; Topology generated from /home/ghahremanpour/Liquids/MOLECULES/OEP/carbon-monoxide/carbon-monoxide-3-oep.log.gz 2 | ; Charge method used esp 3 | ; MOL_GMX.top created by acpype (Rev: 0) on Wed Feb 14 17:43:35 2018 4 | 5 | [ defaults ] 6 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 7 | 1 2 yes 0.5 0.8333 8 | 9 | [ atomtypes ] 10 | ;name bond_type mass charge ptype sigma epsilon Amb 11 | o o 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 12 | c1 c1 0.00000 0.00000 A 3.39967e-01 8.78640e-01 ; 1.91 0.2100 13 | 14 | [ moleculetype ] 15 | ;name nrexcl 16 | MOL 3 17 | 18 | [ atoms ] 19 | ; nr type resi res atom cgnr charge mass ; qtot bond_type 20 | 1 o 1 MOL O1 1 0.006571 16.00000 ; qtot 0.007 21 | 2 c1 1 MOL C1 2 -0.006571 12.01000 ; qtot 0.000 22 | 23 | [ bonds ] 24 | ; ai aj funct r k 25 | 1 2 1 1.1724e-01 6.3438e+05 ; O1 - C1 26 | 27 | [ system ] 28 | MOL 29 | 30 | [ molecules ] 31 | ; Compound nmols 32 | MOL 1 33 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/carbon-monoxide/traj.trr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/GAFF-ESP/carbon-monoxide/traj.trr -------------------------------------------------------------------------------- /examples/GAFF-ESP/quinoline/after_cg.g96: -------------------------------------------------------------------------------- 1 | TITLE 2 | MOL 3 | END 4 | POSITION 5 | 1 MOL C1 1 1.989491608 2.083136783 2.000000000 6 | 1 MOL C2 2 2.111525696 2.152101258 2.000000000 7 | 1 MOL H1 3 2.109641261 2.260461689 2.000000000 8 | 1 MOL C3 4 2.233815877 2.082880057 2.000000000 9 | 1 MOL H2 5 2.327768993 2.137743345 2.000000000 10 | 1 MOL C4 6 2.234467830 1.942503591 2.000000000 11 | 1 MOL H3 7 2.329067111 1.888884835 2.000000000 12 | 1 MOL C5 8 2.113423806 1.871313171 2.000000000 13 | 1 MOL H4 9 2.114539235 1.762564516 2.000000000 14 | 1 MOL C6 10 1.991423863 1.941696339 2.000000000 15 | 1 MOL C7 11 1.869332817 1.872856713 2.000000000 16 | 1 MOL H5 12 1.866263877 1.764139555 2.000000000 17 | 1 MOL C8 13 1.751121784 1.948050276 2.000000000 18 | 1 MOL H6 14 1.654312256 1.899019555 2.000000000 19 | 1 MOL C9 15 1.758522540 2.087881928 2.000000000 20 | 1 MOL H7 16 1.668142335 2.148799614 2.000000000 21 | 1 MOL N1 17 1.875139110 2.153966776 2.000000000 22 | END 23 | BOX 24 | 4.000000000 4.000000000 4.000000000 25 | END 26 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/quinoline/conf.gro: -------------------------------------------------------------------------------- 1 | MOL_GMX.gro created by acpype (Rev: 0) on Wed Feb 14 17:50:25 2018 2 | 17 3 | 1MOL C1 1 1.990 2.082 2.000 4 | 1MOL C2 2 2.113 2.152 2.000 5 | 1MOL H1 3 2.110 2.260 2.000 6 | 1MOL C3 4 2.232 2.083 2.000 7 | 1MOL H2 5 2.326 2.138 2.000 8 | 1MOL C4 6 2.233 1.942 2.000 9 | 1MOL H3 7 2.328 1.890 2.000 10 | 1MOL C5 8 2.116 1.872 2.000 11 | 1MOL H4 9 2.116 1.764 2.000 12 | 1MOL C6 10 1.992 1.940 2.000 13 | 1MOL C7 11 1.867 1.873 2.000 14 | 1MOL H5 12 1.864 1.765 2.000 15 | 1MOL C8 13 1.752 1.947 2.000 16 | 1MOL H6 14 1.654 1.900 2.000 17 | 1MOL C9 15 1.761 2.088 2.000 18 | 1MOL H7 16 1.670 2.148 2.000 19 | 1MOL N1 17 1.874 2.154 2.000 20 | 4.00000 4.00000 4.00000 21 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/quinoline/eigenfreq.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Oct 7 19:53:20 2018 2 | # Created by: 3 | # :-) GROMACS - gmx nmeig, 2019-dev-20181004-83c2c3a2f (double precision) (-: 4 | # 5 | # Executable: /Users/spoel/software-master/bin/gmx_mpi_d 6 | # Data prefix: /Users/spoel/software-master 7 | # Working dir: /Users/spoel/Liquids/FORCE_FIELD/THERMO/GAFF-ESP/quinoline 8 | # Command line: 9 | # gmx_mpi_d nmeig -maxspec 5000 -s nm -f nm.mtx -sigma 1 -last 500 -scale 1.018000 10 | # gmx nmeig is part of G R O M A C S: 11 | # 12 | # Glycine aRginine prOline Methionine Alanine Cystine Serine 13 | # 14 | @ title "Eigenfrequencies" 15 | @ xaxis label "Eigenvector index" 16 | @ yaxis label "Wavenumber [cm\S-1\N]" 17 | @TYPE xy 18 | @ subtitle "mass weighted" 19 | 1 0 20 | 2 0 21 | 3 0.00170776 22 | 4 0.00229361 23 | 5 0.0559807 24 | 6 0.0740539 25 | 7 203.595 26 | 8 222.401 27 | 9 400.038 28 | 10 410.546 29 | 11 481.806 30 | 12 496.716 31 | 13 516.045 32 | 14 534.007 33 | 15 613.859 34 | 16 679.874 35 | 17 759.156 36 | 18 771.933 37 | 19 803.308 38 | 20 804.796 39 | 21 835.637 40 | 22 936.091 41 | 23 946.471 42 | 24 993.218 43 | 25 1001.92 44 | 26 1050.8 45 | 27 1089.68 46 | 28 1135.93 47 | 29 1148.96 48 | 30 1165.56 49 | 31 1186.95 50 | 32 1247.27 51 | 33 1291.54 52 | 34 1334.98 53 | 35 1367.73 54 | 36 1498.52 55 | 37 1613.67 56 | 38 1642.22 57 | 39 1711.74 58 | 40 1729.21 59 | 41 1748.52 60 | 42 1799.34 61 | 43 1804.95 62 | 44 1883.94 63 | 45 2958.48 64 | 46 2975.78 65 | 47 2976.54 66 | 48 2977.14 67 | 49 2977.79 68 | 50 2979.01 69 | 51 2981.18 70 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/quinoline/eigenval.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Oct 7 19:53:20 2018 2 | # Created by: 3 | # :-) GROMACS - gmx nmeig, 2019-dev-20181004-83c2c3a2f (double precision) (-: 4 | # 5 | # Executable: /Users/spoel/software-master/bin/gmx_mpi_d 6 | # Data prefix: /Users/spoel/software-master 7 | # Working dir: /Users/spoel/Liquids/FORCE_FIELD/THERMO/GAFF-ESP/quinoline 8 | # Command line: 9 | # gmx_mpi_d nmeig -maxspec 5000 -s nm -f nm.mtx -sigma 1 -last 500 -scale 1.018000 10 | # gmx nmeig is part of G R O M A C S: 11 | # 12 | # Gyas ROwers Mature At Cryogenic Speed 13 | # 14 | @ title "Eigenvalues" 15 | @ xaxis label "Eigenvalue index" 16 | @ yaxis label "Eigenvalue [Gromacs units]" 17 | @TYPE xy 18 | @ subtitle "mass weighted" 19 | 1 -8.71957e-05 20 | 2 -3.20104e-07 21 | 3 1.03479e-07 22 | 4 1.86655e-07 23 | 5 0.000111193 24 | 6 0.000194579 25 | 7 1470.74 26 | 8 1754.99 27 | 9 5678.12 28 | 10 5980.32 29 | 11 8236.56 30 | 12 8754.21 31 | 13 9448.81 32 | 14 10118 33 | 15 13370.2 34 | 16 16400.5 35 | 17 20448.6 36 | 18 21142.7 37 | 19 22896.3 38 | 20 22981.2 39 | 21 24776.3 40 | 22 31091.2 41 | 23 31784.5 42 | 24 35001.8 43 | 25 35617.6 44 | 26 39178.2 45 | 27 42130.8 46 | 28 45783.1 47 | 29 46839 48 | 30 48202.2 49 | 31 49987.8 50 | 32 55197.9 51 | 33 59185.9 52 | 34 63234.4 53 | 35 66374.7 54 | 36 79675.7 55 | 37 92391 56 | 38 95690 57 | 39 103962 58 | 40 106095 59 | 41 108478 60 | 42 114876 61 | 43 115593 62 | 44 125932 63 | 45 310555 64 | 46 314198 65 | 47 314359 66 | 48 314484 67 | 49 314623 68 | 50 314880 69 | 51 315339 70 | -------------------------------------------------------------------------------- /examples/GAFF-ESP/quinoline/eigenvec.trr: 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-------------------------------------------------------------------------------- /examples/GAFF-ESP/quinoline/traj.trr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dspoel/IR-Spectra/79aeded1562cc2bafbdbf4d8ca7db2dcbabe5056/examples/GAFF-ESP/quinoline/traj.trr -------------------------------------------------------------------------------- /refs/alfred_refs.bib: -------------------------------------------------------------------------------- 1 | @phdthesis{Mott2012a, 2 | Author = {Mott, Adam}, 3 | Title = {{Calculating Infrared Spectra of Proteins and Other Organic Molecules Based on Normal Modes}}, 4 | School = {{Arizona State University}}, 5 | Year = {{2012}}, 6 | Month = {{04}} 7 | } 8 | 9 | @phdthesis{Bodis2007a, 10 | Author = {Bodis, Lorant}, 11 | Title = {{Quantification of spectral similarity towards automatic spectra verification}}, 12 | School = {{ETH Zürich}}, 13 | Year = {{2007}} 14 | } 15 | 16 | @manual{Bradley2007a, 17 | Author = {Bradley, Michael}, 18 | Title = {{Curve Fitting in Raman and IR Spectroscopy: Basic Theory of Line Shapes and Applications}}, 19 | Organization = {{Thermo Fisher Scientific}}, 20 | Year = "2007" 21 | } 22 | 23 | @article{Carvalho2000a, 24 | Author = {de Carvalho Júnior, Osmar and Meneses, Paulo}, 25 | Year = {{2000}}, 26 | Month = {{01}}, 27 | Title = {{Spectral Correlation Mapper (SCM): An Improvement on the Spectral Angle Mapper (SAM)}} 28 | } 29 | 30 | @inproceedings{Choi2014a, 31 | Author = {Choi, Jonghyun and Cho, Hyunjong and Kwac, Jungsuk and Davis, Larry S.}, 32 | Book-Group-Author = {{IEEE}}, 33 | Title = {{Toward Sparse Coding on Cosine Distance}}, 34 | Booktitle = {{2014 22ND INTERNATIONAL CONFERENCE ON PATTERN RECOGNITION (ICPR)}}, 35 | Series = {{International Conference on Pattern Recognition}}, 36 | Year = {{2014}}, 37 | Pages = {{4423-4428}}, 38 | Note = {{22nd International Conference on Pattern Recognition (ICPR), Swedish Soc Automated Image Anal, Stockholm, SWEDEN, AUG 24-28, 2014}}, 39 | DOI = {{10.1109/ICPR.2014.757}}, 40 | ISSN = {{1051-4651}}, 41 | ISBN = {{978-1-4799-5208-3}}, 42 | Times-Cited = {{2}}, 43 | Unique-ID = {{ISI:000359818004094}} 44 | } 45 | -------------------------------------------------------------------------------- /scripts/CalculateSpectrum/mk_spectrum.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | 3 | import argparse, os 4 | from spectrum_functions import * 5 | 6 | pwd = os.getcwd() 7 | parser = argparse.ArgumentParser(description='Generate the IR-spectrum for a molecule using GROMACS output files.') 8 | parser.add_argument('-i1' , type=str , default=pwd , help='First input molecule directory with conf.gro and topol.top. DEFAULT: working directory') 9 | parser.add_argument('-i2' , type=str , default=None , help='Second input molecule directory. DEFAULT: None') 10 | parser.add_argument('-mnm1' , type=str , default="Molecule 1", help='Name of first molecule. DEFAULT: Molecule 1') 11 | parser.add_argument('-mnm2' , type=str , default="Molecule 2", help='Name of second molecule. DEFAULT: Molecule 2') 12 | parser.add_argument('-mdp' , type=str , default=pwd , help='Input mdp directory with cg.mdp and nm.mdp. DEFAULT: working directory') 13 | parser.add_argument('-o' , type=str , default="spectrum" , help='Output spectrum name. DEFAULT: spectrum') 14 | parser.add_argument('-od' , type=str , default=pwd , help='Output spectrum directory. DEFAULT: working directory') 15 | parser.add_argument('-vmin' , type=int , default=0 , help='Lowest frequency to visualize in spectrum. DEFAULT: 0') 16 | parser.add_argument('-vmax' , type=int , default=4000 , help='Highest frequency to visualize in spectrum. DEFAULT: 4000') 17 | parser.add_argument('-s' , type=float, default=4 , help='Step size on the frequency axis. DEFAULT: 4') 18 | parser.add_argument('-g' , type=float, default=24 , help='Set gamma for Cauchy distribution. DEFAULT: 24') 19 | parser.add_argument('-sigma' , type=float, default=1 , help='Sigma to call run_nm. DEFAULT: 1') 20 | parser.add_argument('-scale' , type=float, default=1 , help='Scale factor to call run_nm. DEFAULT: 1') 21 | parser.add_argument('--log1' , help='Read first molecule from log-file' , action='store_true') 22 | parser.add_argument('--log2' , help='Read second molecule from log-file' , action='store_true') 23 | parser.add_argument('--no_nm' , help='Do not run nm' , action='store_true') 24 | parser.add_argument('--linear1', help='Molecule is linear' , action='store_true') 25 | parser.add_argument('--linear2', help='Molecule is linear' , action='store_true') 26 | parser.add_argument('--header' , help='CSV file is generated without a header', action='store_false') 27 | parser.add_argument('--csv' , help='Generate the spectrum as a CSV' , action='store_true') 28 | parser.add_argument('--png' , help='Generate the spectrum as a PNG' , action='store_true') 29 | parser.add_argument('--pdf' , help='Generate the spectrum as a PDF' , action='store_true') 30 | parser.add_argument('--svg' , help='Generate the spectrum as a SVG' , action='store_true') 31 | 32 | if __name__ == "__main__": 33 | 34 | args = parser.parse_args() 35 | 36 | molecule_path1 = args.i1 37 | molecule_path2 = args.i2 38 | molecule_name1 = args.mnm1 39 | molecule_name2 = args.mnm2 40 | mdpdir = args.mdp 41 | outname = args.o 42 | outdir = args.od 43 | no_nm = args.no_nm 44 | start = args.vmin 45 | stop = args.vmax 46 | step_size = args.s 47 | gamma = args.g 48 | log1 = args.log1 49 | log2 = args.log2 50 | linear1 = args.linear1 51 | linear2 = args.linear2 52 | header = args.header 53 | generate_csv = args.csv 54 | generate_png = args.png 55 | generate_pdf = args.pdf 56 | generate_svg = args.svg 57 | sigma = args.sigma 58 | scale_factor = args.scale 59 | 60 | if not no_nm: 61 | run_one_nm(True, sigma, scale_factor, mdpdir, "nm_output") 62 | 63 | save_spectrum(molecule_path1, molecule_name1, linear1, log1, 64 | molecule_path2, molecule_name2, linear2, log2, 65 | start, stop, step_size, gamma, outdir, outname, 66 | header, generate_csv, generate_png, generate_pdf, 67 | generate_svg) 68 | 69 | -------------------------------------------------------------------------------- /scripts/CalculateSpectrum/spectrum_classes.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from numpy import linalg as la 3 | 4 | class Atom: 5 | """Atom class for GROMACS normal mode calculations""" 6 | 7 | def __init__(self, squared_mass, charge_mass_ratio): 8 | """Initialize an Atom object""" 9 | self.__squared_mass = squared_mass 10 | self.__charge_mass_ratio = charge_mass_ratio 11 | 12 | def squared_mass(self): 13 | """Return the squared atomic mass of an Atom""" 14 | return self.__squared_mass 15 | 16 | def charge_mass_ratio(self): 17 | """Return the ratio consisting of the atomic charge divided by the square root of the atomic mass of an Atom""" 18 | return self.__charge_mass_ratio 19 | 20 | class NormalMode: 21 | """NormalMode class for GROMACS normal mode calculations""" 22 | 23 | def __init__(self, eigenfrequency, eigenvector): 24 | """Initialize a NormalMode object""" 25 | self.__eigenfrequency = eigenfrequency 26 | self.__eigenvector = eigenvector 27 | self.__eigenvector_converted_and_normalized = False 28 | self.__intensity = None 29 | 30 | def eigenfrequency(self): 31 | """Return the eigenfrequency of the NormalMode""" 32 | return self.__eigenfrequency 33 | 34 | def intensity(self): 35 | """Return the intensity of the NormalMode""" 36 | return self.__intensity 37 | 38 | def convert_from_cartesian_and_normalize(self, atoms): 39 | """Convert from Cartesian back to mass-weighted coordinates and normalize the eigenvectors""" 40 | if not self.__eigenvector_converted_and_normalized: 41 | for i, atom in enumerate(atoms): 42 | self.__eigenvector[i,:] = self.__eigenvector[i,:]*atom.squared_mass() 43 | self.__eigenvector = self.__eigenvector/la.norm(self.__eigenvector) 44 | self.__eigenvector_converted_and_normalized = True 45 | 46 | def calculate_intensity(self, atoms): 47 | """Calculate intensity of a NormalMode""" 48 | if self.__intensity: 49 | raise Exception("the intensity is already calculated for this NormalMode") 50 | else: 51 | if not self.__eigenvector_converted_and_normalized: 52 | self.convert_from_cartesian_and_normalize(atoms) 53 | # get charge mass ratios 54 | charge_mass_ratios = np.empty([0,0]) 55 | for atom in atoms: 56 | charge_mass_ratios = np.append(charge_mass_ratios, atom.charge_mass_ratio()) 57 | # iterate over dimensions 58 | intensity = 0 59 | for k in range(3): 60 | intensity += (charge_mass_ratios.dot(self.__eigenvector[:,k]))**2 61 | self.__intensity = intensity 62 | 63 | class Molecule: 64 | """Molecule class for GROMACS normal mode calculations""" 65 | 66 | def __init__(self, linear, atoms, normal_modes): 67 | """Initialize a Molecule object""" 68 | self.__atoms = atoms 69 | self.__normal_modes = None 70 | if linear: 71 | self.__normal_modes = normal_modes[5:] 72 | else: 73 | self.__normal_modes = normal_modes[6:] 74 | 75 | def atoms(self): 76 | """Return a list of Atom objects in Molecule""" 77 | return self.__atoms 78 | 79 | def normal_modes(self): 80 | """Return a list of NormalMode objects in Molecule""" 81 | return self.__normal_modes 82 | -------------------------------------------------------------------------------- /scripts/GenerateSpectra/get_exp_data.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | # -*- coding: utf-8 -*- 3 | 4 | import argparse, os, sys, urllib.request, sqlite3, csv, math 5 | from dbutils import * 6 | from mol_csv_api import * 7 | from organic import is_organic 8 | from enum import Enum 9 | from spectrum_functions import * 10 | from pathlib import Path 11 | 12 | if __name__ == "__main__": 13 | 14 | DB = DbUtils('/home/spoel/Liquids/DATABASE/molecules.sqlite3.dat', False) 15 | molecules = [] 16 | CAS_registry_numbers = [] 17 | for row in DB.cursor.execute("SELECT filename, cas FROM molecules"): 18 | molecules.append(str(row[0]).split('.')[0]) 19 | CAS_registry_numbers.append(str(row[1])) 20 | print(CAS_registry_numbers) 21 | print(len(CAS_registry_numbers)) 22 | 23 | 24 | outpath = "/home/alfred/JCAMP-DX/" 25 | for i, molecule in enumerate(molecules): 26 | CAS_registry_number = CAS_registry_numbers[i] 27 | numbers = CAS_registry_number.split(';') 28 | for number in numbers: 29 | url = 'https://webbook.nist.gov/cgi/cbook.cgi?ID=%s&Units=SI&cIR=on' % (number.replace(" ","")) 30 | response = urllib.request.urlopen(url) 31 | data = response.read() 32 | text = data.decode('utf-8') 33 | lines = text.splitlines() 34 | for line in lines: 35 | if "Download %s" % (gmx, tpr, mtz, sigma, output))) 32 | 33 | run_one_nm(True, 1, 1, "output") 34 | --------------------------------------------------------------------------------