├── GAML ├── __init__.py ├── scripts │ └── bash_genTopfiles.sh ├── function_gen_range.py ├── file_gen_scripts.py └── main.py ├── doc ├── GAML.pdf └── Proof_for_Simulation_Time.pdf ├── MANIFEST.in ├── sample ├── test_FSS_analysis │ ├── FSS_analysis-1.png │ └── settingfile.txt ├── test_file_gen_gaussian │ ├── GaussInput_namelist-1.txt │ ├── settingfile.txt │ ├── GaussInput-1.com │ └── GaussInput-2.com ├── test_file_gen_gromacstop │ ├── GenGromacsTopfile_NameList-1.txt │ └── settingfile.txt ├── test_charge_gen_range │ ├── settingfile.txt │ └── ChargeGenRange.txt ├── README.md ├── test_charge_gen_scheme │ ├── settingfile.txt │ ├── BPYR_ChargeGenRange_BF4_ESP.txt │ └── ChargeRandomGen.txt └── test_GAML │ ├── settingfile.txt │ └── BPYR_ChargeGenRange_BF4_ESP.txt ├── .gitignore ├── Solvents ├── formaldehyde │ ├── formaldehyde.pdb │ └── formaldehyde.itp ├── chloroform │ ├── chloroform.pdb │ └── chloroform.itp ├── dibromomethane │ ├── dibromomethane.pdb │ └── dibromomethane.itp ├── dichloromethane │ ├── dichloromethane.pdb │ └── dichloromethane.itp ├── methanol │ ├── methanol.pdb │ └── methanol.itp ├── acetaldehyde │ ├── acetaldehyde.pdb │ └── acetaldehyde.itp ├── nitromethane │ ├── nitromethane.pdb │ └── nitromethane.itp ├── aceticAcid │ ├── aceticAcid.pdb │ └── aceticAcid.itp ├── bromoethane │ ├── bromoethane.pdb │ └── bromoethane.itp ├── ethylchloride │ ├── ethylchloride.pdb │ └── ethylchloride.itp ├── methylformate │ ├── methylformate.pdb │ └── methylformate.itp ├── 1,1-dichloroethane │ └── 1,1-dichloroethane.pdb ├── 1,2-dibromoethane │ ├── 1,2-dibromoethane.pdb │ └── 1,2-dibromoethane.itp ├── 1,2-dichloroethane │ └── 1,2-dichloroethane.pdb ├── pentachloroethane │ ├── pentachloroethane.pdb │ └── pentachloroethane.itp ├── 1,1,2-trichloroethane │ └── 1,1,2-trichloroethane.pdb ├── 1,1,2,2-tetrachloroethane │ └── 1,1,2,2-tetrachloroethane.pdb ├── ethanol │ └── ethanol.pdb ├── acetamide │ └── acetamide.pdb ├── ethanethiol │ └── ethanethiol.pdb ├── dimethylether │ ├── dimethylether.pdb │ └── dimethylether.itp ├── propionitrile │ └── propionitrile.pdb ├── dimethylsulfide │ ├── dimethylsulfide.pdb │ └── dimethylsulfide.itp ├── thiophene │ └── thiophene.pdb ├── acetone │ └── acetone.pdb ├── nitroethane │ └── nitroethane.pdb ├── dimethylsulfoxide │ └── dimethylsulfoxide.pdb ├── methylacetate │ └── methylacetate.pdb ├── 1-bromopropane │ └── 1-bromopropane.pdb ├── pyridine │ └── pyridine.pdb ├── 1,3-dichloropropane │ └── 1,3-dichloropropane.pdb ├── benzene │ └── benzene.pdb ├── N-methylacetamide │ └── N-methylacetamide.pdb ├── bromobenzene │ └── bromobenzene.pdb ├── fluorobenzene │ └── fluorobenzene.pdb ├── N,N-dimethylformamide │ └── N,N-dimethylformamide.pdb ├── 1-propanamine │ └── 1-propanamine.pdb ├── 1-nitropropane │ └── 1-nitropropane.pdb ├── 2-nitropropane │ └── 2-nitropropane.pdb ├── phenol │ └── phenol.pdb ├── benzenthiol │ └── benzenthiol.pdb ├── benzonitrile │ └── benzonitrile.pdb ├── tetrahydrofuran │ └── tetrahydrofuran.pdb ├── ethylacetate │ └── ethylacetate.pdb ├── 1-bromobutane │ └── 1-bromobutane.pdb ├── 1-chlorobutane │ └── 1-chlorobutane.pdb ├── aniline │ └── aniline.pdb ├── 1,4-dichlorobutane │ └── 1,4-dichlorobutane.pdb ├── nitrobenzene │ └── nitrobenzene.pdb ├── cyclopentanone │ └── cyclopentanone.pdb ├── 2-chloroaniline │ └── 2-chloroaniline.pdb ├── 3-methylpyridine │ └── 3-methylpyridine.pdb ├── 4-methylpyridine │ └── 4-methylpyridine.pdb ├── 1-cyclopropylethanone │ └── 1-cyclopropylethanone.pdb ├── 1-butanol │ └── 1-butanol.pdb ├── diethylsulfide │ └── diethylsulfide.pdb ├── n-butanethiol │ └── n-butanethiol.pdb ├── pentanenitrile │ └── pentanenitrile.pdb ├── toluene │ └── toluene.pdb ├── morpholine │ └── morpholine.pdb ├── tert-butylalcohol │ └── tert-butylalcohol.pdb ├── N,N-dimethylacetamide │ └── N,N-dimethylacetamide.pdb ├── 1-butanamine │ └── 1-butanamine.pdb ├── anisole │ └── anisole.pdb ├── styrene │ └── styrene.pdb ├── N-ethylethanamine │ └── N-ethylethanamine.pdb ├── 2-methylphenol │ └── 2-methylphenol.pdb ├── 4-methylphenol │ └── 4-methylphenol.pdb ├── benzylalcohol │ └── benzylalcohol.pdb ├── ethylpropionate │ └── ethylpropionate.pdb ├── acetophenone │ └── acetophenone.pdb ├── cyclohexanone │ └── cyclohexanone.pdb ├── quinoline │ └── quinoline.pdb ├── 1-pentanol │ └── 1-pentanol.pdb ├── 2-methyl-2-butanol │ └── 2-methyl-2-butanol.pdb ├── methylbenzoate │ └── methylbenzoate.pdb ├── 2-hexanone │ └── 2-hexanone.pdb ├── cyclohexanamine │ └── cyclohexanamine.pdb ├── diisopropylether │ └── diisopropylether.pdb ├── 2-heptanone │ └── 2-heptanone.pdb ├── triethylamine │ └── triethylamine.pdb ├── 2,4-dimethyl-3-pentanone │ └── 2,4-dimethyl-3-pentanone.pdb ├── N-1-methylethyl--2-propanamine │ └── N-1-methylethyl--2-propanamine.pdb ├── 1-octanol │ └── 1-octanol.pdb ├── n-butylether │ └── n-butylether.pdb └── N-butyl-1-butanamine │ └── N-butyl-1-butanamine.pdb ├── LICENSE └── setup.py /GAML/__init__.py: -------------------------------------------------------------------------------- 1 | __version__ = '1.2' 2 | -------------------------------------------------------------------------------- /doc/GAML.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/orlandoacevedo/GAML/HEAD/doc/GAML.pdf -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include LICENSE 2 | recursive-include doc * 3 | recursive-include sample * 4 | 5 | -------------------------------------------------------------------------------- /doc/Proof_for_Simulation_Time.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/orlandoacevedo/GAML/HEAD/doc/Proof_for_Simulation_Time.pdf -------------------------------------------------------------------------------- /sample/test_FSS_analysis/FSS_analysis-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/orlandoacevedo/GAML/HEAD/sample/test_FSS_analysis/FSS_analysis-1.png -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | __pycache__/ 2 | 3 | # Distribution / packaging 4 | .Python 5 | build/ 6 | develop-eggs/ 7 | dist/ 8 | downloads/ 9 | eggs/ 10 | .eggs/ 11 | *.egg-info/ 12 | *.egg 13 | .cache 14 | 15 | 16 | -------------------------------------------------------------------------------- /sample/test_file_gen_gaussian/GaussInput_namelist-1.txt: -------------------------------------------------------------------------------- 1 | # Collection of generated file names 2 | 3 | # The topfile is: 4 | # bpyr_bf4_scale08.top 5 | 6 | # The pdbfile is: 7 | # BPYR_BF4_prod_10ns_trr.pdb 8 | 9 | # The select_range is < 10.0 > Angstrom 10 | # Reference format: [residue-index, molecule-index] 11 | 12 | 1 : [2,247] [1,1] 13 | 2 : [2,251] [1,2] 14 | -------------------------------------------------------------------------------- /sample/test_file_gen_gaussian/settingfile.txt: -------------------------------------------------------------------------------- 1 | command = file_gen_gaussian 2 | toppath = bpyr_bf4_scale08.top 3 | file_path = BPYR_BF4_prod_10ns_trr.pdb 4 | gennm = 2 # default is 5 5 | select_range = 10 # default is 10 6 | fname = GaussInput 7 | basis_set = # HF/6-31G(d) Pop=CHelpG # the first '#' is not treated like comment 8 | charge_spin = 0 1 9 | 10 | -------------------------------------------------------------------------------- /sample/test_file_gen_gromacstop/GenGromacsTopfile_NameList-1.txt: -------------------------------------------------------------------------------- 1 | # The collection of all GROMACS topfile names 2 | # The topfile used is: 3 | # bpyr_bf4_scale08.top 4 | # The charge_file used is: 5 | # BPYR_anion_ChargePairs.txt 6 | 7 | # The symmetry_list used is: 8 | # [[1, 9], [2, 10], [3, 7], [4, 8], [13, 14], [16, 17, 19, 20], [22, 23, 24], [15, 18], 5, 6, 11, 12, 21] 9 | 10 | GenGromacsTopfile-1.top 11 | GenGromacsTopfile-2.top 12 | -------------------------------------------------------------------------------- /sample/test_FSS_analysis/settingfile.txt: -------------------------------------------------------------------------------- 1 | command = fss_analysis 2 | file_path = BPYR_Charge_HvapMAE_1.txt 3 | atomtype_list = ['CY','HY','CW','HW','HA','HS','HT','CS','CR','HR','NA','CA','CT'] 4 | stepsize = 0.01 5 | error_tolerance = 0.30 6 | bool_abscomp = False 7 | percent = 0.95 8 | cut_keyword = MAE 9 | pallette_nm = 50 10 | color_map = rainbow 11 | fname = FSS_analysis 12 | 13 | 14 | -------------------------------------------------------------------------------- /sample/test_file_gen_gromacstop/settingfile.txt: -------------------------------------------------------------------------------- 1 | command = file_gen_gromacstop 2 | toppath = bpyr_bf4_scale08.top 3 | charge_path = BPYR_anion_ChargePairs.txt 4 | symmetry_list = [[1,9],[2,10],[3, 7],[4,8],[13,14],[ 16,17,19,20],[22 ,23,24],[15,18],5,6,11,12,21] 5 | reschoose = 6 | fname = GenGromacsTopfile 7 | gennm = 2 # default is None 8 | in_keyword = PAIR 9 | cut_keyword = # default is MAE 10 | 11 | -------------------------------------------------------------------------------- /sample/test_charge_gen_range/settingfile.txt: -------------------------------------------------------------------------------- 1 | command = charge_gen_range # command to execute, required 2 | charge_path = BPYR_BF4_charge_collection.txt # input file path, required 3 | atomnm = 24 # the processed atom number, required 4 | percent = 0.8 # optional, default is 0.8 5 | stepsize = 0.01 # optional, default is 0.01 6 | nmround = 3 # optional, default is 3 7 | fname = ChargeGenRange # optional, default is ChargeGenRange 8 | -------------------------------------------------------------------------------- /sample/README.md: -------------------------------------------------------------------------------- 1 | # Samples 2 | 3 | This folder contains all the sample files, which can be either used for testing or templates. 4 | 5 | For each specific function, either can be executed by loading the corresponded settingfile or by inputting in the command-line. 6 | 7 | 8 | For settingfile, < # > is chosen as the comments, except for the 'basis_set' parameter, the first # is not. 9 | By using settingfile, one of the greatest advantages is that you can process different command blocks at the same time. 10 | 11 | 12 | For the command-line input, please use command `gaml` or `gaml -h` or `gaml [command] -h` to get help information. 13 | 14 | -------------------------------------------------------------------------------- /Solvents/formaldehyde/formaldehyde.pdb: -------------------------------------------------------------------------------- 1 | TITLE formaldehyde 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 O01 MOL 1 -0.225 1.000 0.000 14 | ATOM 3 H02 MOL 1 1.586 1.000 -0.933 15 | ATOM 4 H03 MOL 1 1.586 1.001 0.933 16 | TER 17 | CONECT 1 2 18 | CONECT 1 3 19 | CONECT 1 4 20 | END 21 | -------------------------------------------------------------------------------- /sample/test_charge_gen_scheme/settingfile.txt: -------------------------------------------------------------------------------- 1 | command = charge_gen_scheme 2 | charge_path = BPYR_ChargeGenRange_BF4_ESP.txt 3 | symmetry_list = [[1,9],[2,10],[3,7], [4,8], [13,14],[16,17,19,20],[22,23,24],[15,18],5,6,11,12,21] # default is None 4 | offset_list = [1,11] # default is None 5 | counter_list = [[15,16], [22,21]] # default is None 6 | gennm = # default is 5 7 | nmround = 3 # default is 2 8 | total_charge = 0.8 # default is 0.0 9 | fname = # default is ChargeRandomGen 10 | threshold = # default is 1.0 11 | offset_nm = # default is 5 12 | bool_neutral = # default is True 13 | bool_nozero = # default is True 14 | pn_limit = # default is None 15 | in_keyword = ATOM # default is ATOM 16 | -------------------------------------------------------------------------------- /Solvents/chloroform/chloroform.pdb: -------------------------------------------------------------------------------- 1 | TITLE chloroform 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 Cl0 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.772 1.000 0.000 14 | ATOM 3 Cl1 MOL 1 -1.392 1.000 1.659 15 | ATOM 4 Cl2 MOL 1 -1.394 2.395 -0.898 16 | ATOM 5 H04 MOL 1 -1.115 0.088 -0.495 17 | TER 18 | CONECT 1 2 19 | CONECT 2 3 20 | CONECT 2 4 21 | CONECT 2 5 22 | END 23 | -------------------------------------------------------------------------------- /Solvents/dibromomethane/dibromomethane.pdb: -------------------------------------------------------------------------------- 1 | TITLE dibromomethane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 Br0 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.933 1.000 0.000 14 | ATOM 3 Br2 MOL 1 -1.700 1.000 1.775 15 | ATOM 4 H03 MOL 1 -1.273 0.101 -0.518 16 | ATOM 5 H04 MOL 1 -1.273 1.899 -0.518 17 | TER 18 | CONECT 1 2 19 | CONECT 2 3 20 | CONECT 2 4 21 | CONECT 2 5 22 | END 23 | -------------------------------------------------------------------------------- /Solvents/dichloromethane/dichloromethane.pdb: -------------------------------------------------------------------------------- 1 | TITLE dichloromethane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 Cl0 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.767 1.000 0.000 14 | ATOM 3 Cl1 MOL 1 -1.404 1.000 1.649 15 | ATOM 4 H03 MOL 1 -1.123 0.106 -0.518 16 | ATOM 5 H04 MOL 1 -1.122 1.894 -0.518 17 | TER 18 | CONECT 1 2 19 | CONECT 2 3 20 | CONECT 2 4 21 | CONECT 2 5 22 | END 23 | -------------------------------------------------------------------------------- /Solvents/methanol/methanol.pdb: -------------------------------------------------------------------------------- 1 | TITLE methanol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 O01 MOL 1 -0.416 1.000 0.000 14 | ATOM 3 H02 MOL 1 1.364 1.000 -1.030 15 | ATOM 4 H03 MOL 1 1.364 0.115 0.527 16 | ATOM 5 H04 MOL 1 1.354 1.899 0.510 17 | ATOM 6 H05 MOL 1 -0.701 0.192 -0.460 18 | TER 19 | CONECT 1 2 20 | CONECT 1 3 21 | CONECT 1 4 22 | CONECT 1 5 23 | CONECT 2 6 24 | END 25 | -------------------------------------------------------------------------------- /sample/test_GAML/settingfile.txt: -------------------------------------------------------------------------------- 1 | command = gaml 2 | file_path = BPYR_Charge_HvapMAE_1.txt 3 | charge_path = BPYR_ChargeGenRange_BF4_ESP.txt 4 | offset_list = [1,11] 5 | counter_list = [[15,16],[22,21]] 6 | symmetry_list = [[1,9],[2,10],[3,7],[4,8],[13,14],[16,17,19,20],[22,23,24],[15,18],5,6,11,12,21] 7 | gennm = 50 # default is 20 8 | nmround = 2 # default is 2 9 | total_charge = 0.8 # default is 1.0 10 | error_tolerance = 0.10 # default is 0.12 11 | fname = 12 | ratio = 0:0:1 # ml:av:mu 13 | charge_extend_by = # default is 0.3 14 | threshold = # default is 1.0 15 | bool_neutral = false # default is True 16 | bool_nozero = # default is True 17 | bool_abscomp = # default is True 18 | pn_limit = 3n 19 | cut_keyword = # default is MAE 20 | 21 | -------------------------------------------------------------------------------- /Solvents/acetaldehyde/acetaldehyde.pdb: -------------------------------------------------------------------------------- 1 | TITLE acetaldehyde 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.497 1.000 0.000 14 | ATOM 3 O02 MOL 1 -1.166 1.000 1.028 15 | ATOM 4 H03 MOL 1 1.358 0.999 -1.033 16 | ATOM 5 H04 MOL 1 1.364 0.101 0.503 17 | ATOM 6 H05 MOL 1 1.364 1.900 0.501 18 | ATOM 7 H06 MOL 1 -0.978 0.999 -0.992 19 | TER 20 | CONECT 1 2 21 | CONECT 2 3 22 | CONECT 1 4 23 | CONECT 1 5 24 | CONECT 1 6 25 | CONECT 2 7 26 | END 27 | -------------------------------------------------------------------------------- /Solvents/nitromethane/nitromethane.pdb: -------------------------------------------------------------------------------- 1 | TITLE nitromethane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 N01 MOL 1 -0.487 1.000 0.000 14 | ATOM 3 O02 MOL 1 -1.054 1.000 1.099 15 | ATOM 4 O03 MOL 1 -1.043 1.001 -1.105 16 | ATOM 5 H04 MOL 1 1.353 1.000 1.033 17 | ATOM 6 H05 MOL 1 1.328 1.902 -0.520 18 | ATOM 7 H06 MOL 1 1.328 0.098 -0.520 19 | TER 20 | CONECT 1 2 21 | CONECT 2 3 22 | CONECT 2 4 23 | CONECT 1 5 24 | CONECT 1 6 25 | CONECT 1 7 26 | END 27 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2018 Orlando Acevedo 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /sample/test_charge_gen_range/ChargeGenRange.txt: -------------------------------------------------------------------------------- 1 | # File charge ranges based on the input charge_file 2 | # The charge file used is: 3 | # BPYR_BF4_charge_collection.txt 4 | # Line is corresponded to each atom 5 | 6 | ATOM 1 0.1350 0.1650 7 | ATOM 2 0.2780 0.2980 8 | ATOM 3 -0.2800 -0.2600 9 | ATOM 4 0.2660 0.2860 10 | ATOM 5 -0.1110 -0.0910 11 | ATOM 6 0.2700 0.2900 12 | ATOM 7 -0.2860 -0.2660 13 | ATOM 8 0.2640 0.2840 14 | ATOM 9 0.1190 0.1490 15 | ATOM 10 0.2700 0.2900 16 | ATOM 11 -0.6020 -0.5520 17 | ATOM 12 -0.2240 -0.1740 18 | ATOM 13 0.2190 0.2390 19 | ATOM 14 0.2150 0.2350 20 | ATOM 15 -0.3640 -0.3340 21 | ATOM 16 0.1670 0.2070 22 | ATOM 17 0.1630 0.2030 23 | ATOM 18 -0.3500 -0.3300 24 | ATOM 19 0.1420 0.1820 25 | ATOM 20 0.1430 0.1830 26 | ATOM 21 -0.5160 -0.4960 27 | ATOM 22 0.1580 0.1880 28 | ATOM 23 0.1510 0.1810 29 | ATOM 24 0.1560 0.1860 30 | -------------------------------------------------------------------------------- /Solvents/aceticAcid/aceticAcid.pdb: -------------------------------------------------------------------------------- 1 | TITLE aceticAcid 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.498 1.000 0.000 14 | ATOM 3 O02 MOL 1 -1.187 1.000 1.007 15 | ATOM 4 O03 MOL 1 -1.021 1.002 -1.247 16 | ATOM 5 H04 MOL 1 1.361 1.000 1.032 17 | ATOM 6 H05 MOL 1 1.370 1.900 -0.498 18 | ATOM 7 H06 MOL 1 1.370 0.100 -0.498 19 | ATOM 8 H07 MOL 1 -0.347 1.002 -1.952 20 | TER 21 | CONECT 1 2 22 | CONECT 2 3 23 | CONECT 2 4 24 | CONECT 1 5 25 | CONECT 1 6 26 | CONECT 1 7 27 | CONECT 4 8 28 | END 29 | -------------------------------------------------------------------------------- /Solvents/bromoethane/bromoethane.pdb: -------------------------------------------------------------------------------- 1 | TITLE bromoethane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.511 1.000 0.000 14 | ATOM 3 Br2 MOL 1 -1.171 1.000 1.829 15 | ATOM 4 H03 MOL 1 1.378 0.999 -1.027 16 | ATOM 5 H04 MOL 1 1.398 0.115 0.508 17 | ATOM 6 H05 MOL 1 1.398 1.886 0.506 18 | ATOM 7 H06 MOL 1 -0.913 0.107 -0.484 19 | ATOM 8 H07 MOL 1 -0.913 1.893 -0.484 20 | TER 21 | CONECT 1 2 22 | CONECT 2 3 23 | CONECT 1 4 24 | CONECT 1 5 25 | CONECT 1 6 26 | CONECT 2 7 27 | CONECT 2 8 28 | END 29 | -------------------------------------------------------------------------------- /sample/test_file_gen_gaussian/GaussInput-1.com: -------------------------------------------------------------------------------- 1 | %chk=GaussInput-1.chk 2 | # HF/6-31G(d) Pop=CHelpG 3 | 4 | GaussInput Charge Analysis 5 | 6 | 0 1 7 | B 23.225 3.206 20.511 8 | F 23.625 3.925 19.395 9 | F 24.205 3.225 21.495 10 | F 22.02 3.778 21.004 11 | F 22.964 1.92 20.155 12 | C 20.863 1.8 18.079 13 | H 21.7 2.462 18.175 14 | C 19.627 1.952 18.644 15 | H 19.495 2.677 19.423 16 | C 18.599 1.05 18.18 17 | H 17.661 1.231 18.671 18 | C 18.8 0.177 17.117 19 | H 18.05 -0.412 16.629 20 | C 20.084 0.152 16.628 21 | H 20.313 -0.587 15.886 22 | N 21.018 0.896 17.113 23 | C 22.366 0.592 16.538 24 | H 22.282 0.132 15.564 25 | H 22.894 1.503 16.302 26 | C 23.163 -0.431 17.315 27 | H 23.182 -0.201 18.378 28 | H 24.192 -0.45 16.964 29 | C 22.648 -1.816 17.157 30 | H 21.621 -1.919 17.498 31 | H 22.62 -1.925 16.076 32 | C 23.538 -2.877 17.64 33 | H 23.232 -3.86 17.302 34 | H 24.598 -2.745 17.456 35 | H 23.563 -2.864 18.723 36 | 37 | 38 | 39 | -------------------------------------------------------------------------------- /sample/test_file_gen_gaussian/GaussInput-2.com: -------------------------------------------------------------------------------- 1 | %chk=GaussInput-2.chk 2 | # HF/6-31G(d) Pop=CHelpG 3 | 4 | GaussInput Charge Analysis 5 | 6 | 0 1 7 | B 45.212 54.037 35.574 8 | F 45.202 53.156 36.662 9 | F 45.434 55.315 36.085 10 | F 46.168 53.647 34.648 11 | F 43.925 54.062 35.018 12 | C 42.364 48.821 28.166 13 | H 43.14 48.841 27.426 14 | C 41.725 47.671 28.546 15 | H 41.994 46.74 28.087 16 | C 40.89 47.577 29.658 17 | H 40.453 46.633 29.925 18 | C 40.641 48.789 30.297 19 | H 39.897 48.765 31.069 20 | C 41.323 49.886 29.874 21 | H 41.098 50.822 30.346 22 | N 42.106 49.929 28.807 23 | C 42.771 51.229 28.386 24 | H 42.871 51.844 29.268 25 | H 43.718 51.003 27.918 26 | C 41.818 51.943 27.349 27 | H 40.829 52.248 27.682 28 | H 41.798 51.336 26.448 29 | C 42.494 53.248 26.851 30 | H 43.006 53.67 27.712 31 | H 43.329 52.934 26.23 32 | C 41.575 54.211 26.212 33 | H 42.195 55.022 25.847 34 | H 40.87 53.829 25.482 35 | H 40.889 54.666 26.917 36 | 37 | 38 | 39 | -------------------------------------------------------------------------------- /Solvents/ethylchloride/ethylchloride.pdb: -------------------------------------------------------------------------------- 1 | TITLE ethylchloride 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.514 1.000 0.000 14 | ATOM 3 Cl0 MOL 1 -1.135 1.000 1.665 15 | ATOM 4 H03 MOL 1 1.377 0.999 -1.028 16 | ATOM 5 H04 MOL 1 1.396 0.112 0.505 17 | ATOM 6 H05 MOL 1 1.396 1.889 0.502 18 | ATOM 7 H06 MOL 1 -0.902 0.111 -0.506 19 | ATOM 8 H07 MOL 1 -0.902 1.889 -0.505 20 | TER 21 | CONECT 1 2 22 | CONECT 2 3 23 | CONECT 1 4 24 | CONECT 1 5 25 | CONECT 1 6 26 | CONECT 2 7 27 | CONECT 2 8 28 | END 29 | -------------------------------------------------------------------------------- /Solvents/methylformate/methylformate.pdb: -------------------------------------------------------------------------------- 1 | TITLE methylformate 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 O01 MOL 1 -0.428 1.000 0.000 14 | ATOM 3 C02 MOL 1 -0.974 1.000 1.241 15 | ATOM 4 O03 MOL 1 -0.369 1.000 2.302 16 | ATOM 5 H04 MOL 1 1.338 0.999 -1.040 17 | ATOM 6 H05 MOL 1 1.383 0.099 0.489 18 | ATOM 7 H06 MOL 1 1.382 1.902 0.487 19 | ATOM 8 H07 MOL 1 -2.071 1.001 1.149 20 | TER 21 | CONECT 1 2 22 | CONECT 2 3 23 | CONECT 3 4 24 | CONECT 1 5 25 | CONECT 1 6 26 | CONECT 1 7 27 | CONECT 3 8 28 | END 29 | -------------------------------------------------------------------------------- /sample/test_GAML/BPYR_ChargeGenRange_BF4_ESP.txt: -------------------------------------------------------------------------------- 1 | # This is the charge_range based on the input charge_file 2 | # The charge file used is BPYR_BF4_charge_collection.txt 3 | # Each line's charge_range is corresponded to each atom 4 | 5 | ATOM 1 0.1350 0.1650 6 | ATOM 2 0.2780 0.2980 7 | ATOM 3 -0.2800 -0.2600 8 | ATOM 4 0.2660 0.2860 9 | ATOM 5 -0.1110 -0.0910 10 | ATOM 6 0.2700 0.2900 11 | ATOM 7 -0.2860 -0.2660 12 | ATOM 8 0.2640 0.2840 13 | ATOM 9 0.1190 0.1490 14 | ATOM 10 0.2700 0.2900 15 | ATOM 11 -0.6020 -0.5520 16 | ATOM 12 -0.2240 -0.1740 17 | ATOM 13 0.2190 0.2390 18 | ATOM 14 0.2150 0.2350 19 | ATOM 15 -0.3640 -0.3340 20 | ATOM 16 0.1670 0.2070 21 | ATOM 17 0.1630 0.2030 22 | ATOM 18 -0.3500 -0.3300 23 | ATOM 19 0.1420 0.1820 24 | ATOM 20 0.1430 0.1830 25 | ATOM 21 -0.5160 -0.4960 26 | ATOM 22 0.1580 0.1880 27 | ATOM 23 0.1510 0.1810 28 | ATOM 24 0.1560 0.1860 29 | -------------------------------------------------------------------------------- /Solvents/1,1-dichloroethane/1,1-dichloroethane.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1,1-dichloroethane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.518 1.000 0.000 14 | ATOM 3 Cl0 MOL 1 -1.134 1.000 1.669 15 | ATOM 4 Cl1 MOL 1 -1.134 2.421 -0.875 16 | ATOM 5 H04 MOL 1 1.389 0.118 0.520 17 | ATOM 6 H05 MOL 1 1.406 1.889 0.496 18 | ATOM 7 H06 MOL 1 1.389 0.976 -1.024 19 | ATOM 8 H07 MOL 1 -0.902 0.106 -0.499 20 | TER 21 | CONECT 1 2 22 | CONECT 2 3 23 | CONECT 2 4 24 | CONECT 1 5 25 | CONECT 1 6 26 | CONECT 1 7 27 | CONECT 2 8 28 | END 29 | -------------------------------------------------------------------------------- /Solvents/1,2-dibromoethane/1,2-dibromoethane.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1,2-dibromoethane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 Br0 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.947 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.452 1.000 1.423 15 | ATOM 4 Br3 MOL 1 -3.399 0.998 1.423 16 | ATOM 5 H04 MOL 1 -1.258 0.108 -0.552 17 | ATOM 6 H05 MOL 1 -1.258 1.892 -0.552 18 | ATOM 7 H06 MOL 1 -1.141 1.892 1.974 19 | ATOM 8 H07 MOL 1 -1.139 0.109 1.975 20 | TER 21 | CONECT 1 2 22 | CONECT 2 3 23 | CONECT 3 4 24 | CONECT 2 5 25 | CONECT 2 6 26 | CONECT 3 7 27 | CONECT 3 8 28 | END 29 | -------------------------------------------------------------------------------- /Solvents/1,2-dichloroethane/1,2-dichloroethane.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1,2-dichloroethane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 Cl0 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.781 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.307 1.000 1.423 15 | ATOM 4 Cl1 MOL 1 -3.088 0.998 1.423 16 | ATOM 5 H04 MOL 1 -1.110 0.111 -0.547 17 | ATOM 6 H05 MOL 1 -1.110 1.889 -0.547 18 | ATOM 7 H06 MOL 1 -0.979 1.890 1.969 19 | ATOM 8 H07 MOL 1 -0.977 0.111 1.970 20 | TER 21 | CONECT 1 2 22 | CONECT 2 3 23 | CONECT 3 4 24 | CONECT 2 5 25 | CONECT 2 6 26 | CONECT 3 7 27 | CONECT 3 8 28 | END 29 | -------------------------------------------------------------------------------- /Solvents/pentachloroethane/pentachloroethane.pdb: -------------------------------------------------------------------------------- 1 | TITLE pentachloroethane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 Cl0 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.804 1.000 0.000 14 | ATOM 3 Cl1 MOL 1 -1.336 1.000 1.719 15 | ATOM 4 C03 MOL 1 -1.425 2.149 -0.842 16 | ATOM 5 Cl2 MOL 1 -0.786 2.146 -2.529 17 | ATOM 6 Cl3 MOL 1 -3.210 1.914 -0.978 18 | ATOM 7 Cl4 MOL 1 -1.125 3.776 -0.140 19 | ATOM 8 H07 MOL 1 -1.101 0.032 -0.406 20 | TER 21 | CONECT 1 2 22 | CONECT 2 3 23 | CONECT 2 4 24 | CONECT 4 5 25 | CONECT 4 6 26 | CONECT 4 7 27 | CONECT 2 8 28 | END 29 | -------------------------------------------------------------------------------- /sample/test_charge_gen_scheme/BPYR_ChargeGenRange_BF4_ESP.txt: -------------------------------------------------------------------------------- 1 | # This is the charge_range based on the input charge_file 2 | # The charge file used is BPYR_BF4_charge_collection.txt 3 | # Each line's charge_range is corresponded to each atom 4 | 5 | ATOM 1 0.1350 0.1650 6 | ATOM 2 0.2780 0.2980 7 | ATOM 3 -0.2800 -0.2600 8 | ATOM 4 0.2660 0.2860 9 | ATOM 5 -0.1110 -0.0910 10 | ATOM 6 0.2700 0.2900 11 | ATOM 7 -0.2860 -0.2660 12 | ATOM 8 0.2640 0.2840 13 | ATOM 9 0.1190 0.1490 14 | ATOM 10 0.2700 0.2900 15 | ATOM 11 -0.6020 -0.5520 16 | ATOM 12 -0.2240 -0.1740 17 | ATOM 13 0.2190 0.2390 18 | ATOM 14 0.2150 0.2350 19 | ATOM 15 -0.3640 -0.3340 20 | ATOM 16 0.1670 0.2070 21 | ATOM 17 0.1630 0.2030 22 | ATOM 18 -0.3500 -0.3300 23 | ATOM 19 0.1420 0.1820 24 | ATOM 20 0.1430 0.1830 25 | ATOM 21 -0.5160 -0.4960 26 | ATOM 22 0.1580 0.1880 27 | ATOM 23 0.1510 0.1810 28 | ATOM 24 0.1560 0.1860 29 | -------------------------------------------------------------------------------- /Solvents/1,1,2-trichloroethane/1,1,2-trichloroethane.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1,1,2-trichloroethane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 Cl0 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.786 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.360 1.000 1.413 15 | ATOM 4 Cl1 MOL 1 -1.010 2.524 2.274 16 | ATOM 5 Cl2 MOL 1 -3.133 0.778 1.342 17 | ATOM 6 H05 MOL 1 -1.092 0.100 -0.543 18 | ATOM 7 H06 MOL 1 -1.116 1.873 -0.574 19 | ATOM 8 H07 MOL 1 -0.952 0.178 2.008 20 | TER 21 | CONECT 1 2 22 | CONECT 2 3 23 | CONECT 3 4 24 | CONECT 3 5 25 | CONECT 2 6 26 | CONECT 2 7 27 | CONECT 3 8 28 | END 29 | -------------------------------------------------------------------------------- /Solvents/1,1,2,2-tetrachloroethane/1,1,2,2-tetrachloroethane.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1,1,2,2-tetrachloroethane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 Cl0 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.796 1.000 0.000 14 | ATOM 3 Cl1 MOL 1 -1.318 1.000 1.719 15 | ATOM 4 C03 MOL 1 -1.366 2.200 -0.771 16 | ATOM 5 Cl2 MOL 1 -0.841 2.201 -2.488 17 | ATOM 6 Cl3 MOL 1 -3.163 2.199 -0.772 18 | ATOM 7 H06 MOL 1 -1.119 0.050 -0.436 19 | ATOM 8 H07 MOL 1 -1.042 3.149 -0.332 20 | TER 21 | CONECT 1 2 22 | CONECT 2 3 23 | CONECT 2 4 24 | CONECT 4 5 25 | CONECT 4 6 26 | CONECT 2 7 27 | CONECT 4 8 28 | END 29 | -------------------------------------------------------------------------------- /Solvents/ethanol/ethanol.pdb: -------------------------------------------------------------------------------- 1 | TITLE ethanol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.515 1.000 0.000 14 | ATOM 3 O02 MOL 1 -0.999 1.000 1.335 15 | ATOM 4 H03 MOL 1 1.389 1.001 -1.022 16 | ATOM 5 H04 MOL 1 1.387 0.119 0.523 17 | ATOM 6 H05 MOL 1 1.385 1.880 0.526 18 | ATOM 7 H06 MOL 1 -0.907 0.118 -0.516 19 | ATOM 8 H07 MOL 1 -0.897 1.894 -0.501 20 | ATOM 9 H08 MOL 1 -0.661 0.198 1.769 21 | TER 22 | CONECT 1 2 23 | CONECT 2 3 24 | CONECT 1 4 25 | CONECT 1 5 26 | CONECT 1 6 27 | CONECT 2 7 28 | CONECT 2 8 29 | CONECT 3 9 30 | END 31 | -------------------------------------------------------------------------------- /Solvents/acetamide/acetamide.pdb: -------------------------------------------------------------------------------- 1 | TITLE acetamide 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.502 1.000 0.000 14 | ATOM 3 N02 MOL 1 -1.088 1.000 1.229 15 | ATOM 4 O03 MOL 1 -1.172 0.999 -1.025 16 | ATOM 5 H04 MOL 1 1.402 1.000 1.017 17 | ATOM 6 H05 MOL 1 1.357 1.895 -0.516 18 | ATOM 7 H06 MOL 1 1.357 0.105 -0.516 19 | ATOM 8 H07 MOL 1 -0.568 1.000 2.094 20 | ATOM 9 H08 MOL 1 -2.099 1.001 1.265 21 | TER 22 | CONECT 1 2 23 | CONECT 2 3 24 | CONECT 2 4 25 | CONECT 1 5 26 | CONECT 1 6 27 | CONECT 1 7 28 | CONECT 3 8 29 | CONECT 3 9 30 | END 31 | -------------------------------------------------------------------------------- /Solvents/ethanethiol/ethanethiol.pdb: -------------------------------------------------------------------------------- 1 | TITLE ethanethiol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.517 1.000 0.000 14 | ATOM 3 S02 MOL 1 -1.158 1.000 1.697 15 | ATOM 4 H03 MOL 1 1.372 1.001 -1.030 16 | ATOM 5 H04 MOL 1 1.401 0.109 0.495 17 | ATOM 6 H05 MOL 1 1.401 1.889 0.498 18 | ATOM 7 H06 MOL 1 -0.895 0.114 -0.520 19 | ATOM 8 H07 MOL 1 -0.894 1.888 -0.517 20 | ATOM 9 H08 MOL 1 -0.626 -0.176 2.063 21 | TER 22 | CONECT 1 2 23 | CONECT 2 3 24 | CONECT 1 4 25 | CONECT 1 5 26 | CONECT 1 6 27 | CONECT 2 7 28 | CONECT 2 8 29 | CONECT 3 9 30 | END 31 | -------------------------------------------------------------------------------- /Solvents/dimethylether/dimethylether.pdb: -------------------------------------------------------------------------------- 1 | TITLE dimethylether 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 O01 MOL 1 -0.421 1.000 0.000 14 | ATOM 3 C02 MOL 1 -0.942 1.000 1.322 15 | ATOM 4 H03 MOL 1 1.344 1.001 -1.038 16 | ATOM 5 H04 MOL 1 1.382 0.102 0.494 17 | ATOM 6 H05 MOL 1 1.382 1.897 0.497 18 | ATOM 7 H06 MOL 1 -2.033 0.999 1.262 19 | ATOM 8 H07 MOL 1 -0.622 1.898 1.859 20 | ATOM 9 H08 MOL 1 -0.619 0.103 1.860 21 | TER 22 | CONECT 1 2 23 | CONECT 2 3 24 | CONECT 1 4 25 | CONECT 1 5 26 | CONECT 1 6 27 | CONECT 3 7 28 | CONECT 3 8 29 | CONECT 3 9 30 | END 31 | -------------------------------------------------------------------------------- /Solvents/propionitrile/propionitrile.pdb: -------------------------------------------------------------------------------- 1 | TITLE propionitrile 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.518 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.051 1.000 1.423 15 | ATOM 4 N03 MOL 1 -1.496 1.000 2.603 16 | ATOM 5 H04 MOL 1 1.380 0.999 -1.026 17 | ATOM 6 H05 MOL 1 1.394 0.115 0.511 18 | ATOM 7 H06 MOL 1 1.394 1.886 0.509 19 | ATOM 8 H07 MOL 1 -0.892 0.114 -0.523 20 | ATOM 9 H08 MOL 1 -0.892 1.886 -0.523 21 | TER 22 | CONECT 1 2 23 | CONECT 2 3 24 | CONECT 3 4 25 | CONECT 1 5 26 | CONECT 1 6 27 | CONECT 1 7 28 | CONECT 2 8 29 | CONECT 2 9 30 | END 31 | -------------------------------------------------------------------------------- /Solvents/dimethylsulfide/dimethylsulfide.pdb: -------------------------------------------------------------------------------- 1 | TITLE dimethylsulfide 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 S01 MOL 1 -0.808 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.077 1.000 1.788 15 | ATOM 4 H03 MOL 1 1.359 1.001 -1.033 16 | ATOM 5 H04 MOL 1 1.380 0.105 0.499 17 | ATOM 6 H05 MOL 1 1.380 1.894 0.502 18 | ATOM 7 H06 MOL 1 -2.151 0.999 1.991 19 | ATOM 8 H07 MOL 1 -0.639 1.895 2.238 20 | ATOM 9 H08 MOL 1 -0.637 0.106 2.238 21 | TER 22 | CONECT 1 2 23 | CONECT 2 3 24 | CONECT 1 4 25 | CONECT 1 5 26 | CONECT 1 6 27 | CONECT 3 7 28 | CONECT 3 8 29 | CONECT 3 9 30 | END 31 | -------------------------------------------------------------------------------- /Solvents/thiophene/thiophene.pdb: -------------------------------------------------------------------------------- 1 | TITLE thiophene 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.425 1.000 0.000 14 | ATOM 3 C02 MOL 1 -0.941 1.000 1.278 15 | ATOM 4 S03 MOL 1 0.290 1.000 2.467 16 | ATOM 5 C04 MOL 1 1.516 1.000 1.278 17 | ATOM 6 H05 MOL 1 1.614 1.001 -0.892 18 | ATOM 7 H06 MOL 1 -1.040 1.001 -0.892 19 | ATOM 8 H07 MOL 1 -1.981 0.999 1.572 20 | ATOM 9 H08 MOL 1 2.556 1.001 1.572 21 | TER 22 | CONECT 1 2 23 | CONECT 2 3 24 | CONECT 3 4 25 | CONECT 1 5 26 | CONECT 1 6 27 | CONECT 2 7 28 | CONECT 3 8 29 | CONECT 5 9 30 | CONECT 4 5 31 | END 32 | -------------------------------------------------------------------------------- /Solvents/acetone/acetone.pdb: -------------------------------------------------------------------------------- 1 | TITLE acetone 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.505 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.217 1.000 1.326 15 | ATOM 4 O03 MOL 1 -1.136 0.999 -1.058 16 | ATOM 5 H04 MOL 1 1.395 1.000 1.019 17 | ATOM 6 H05 MOL 1 1.358 1.897 -0.511 18 | ATOM 7 H06 MOL 1 1.358 0.103 -0.512 19 | ATOM 8 H07 MOL 1 -0.507 1.000 2.156 20 | ATOM 9 H08 MOL 1 -1.837 0.103 1.399 21 | ATOM 10 H09 MOL 1 -1.837 1.897 1.399 22 | TER 23 | CONECT 1 2 24 | CONECT 2 3 25 | CONECT 2 4 26 | CONECT 1 5 27 | CONECT 1 6 28 | CONECT 1 7 29 | CONECT 3 8 30 | CONECT 3 9 31 | CONECT 3 10 32 | END 33 | -------------------------------------------------------------------------------- /Solvents/nitroethane/nitroethane.pdb: -------------------------------------------------------------------------------- 1 | TITLE nitroethane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.514 1.000 0.000 14 | ATOM 3 N02 MOL 1 -0.989 1.000 1.420 15 | ATOM 4 O03 MOL 1 -1.169 -0.102 1.952 16 | ATOM 5 O04 MOL 1 -1.165 2.102 1.954 17 | ATOM 6 H05 MOL 1 1.377 1.001 -1.028 18 | ATOM 7 H06 MOL 1 1.398 0.114 0.506 19 | ATOM 8 H07 MOL 1 1.399 1.884 0.508 20 | ATOM 9 H08 MOL 1 -0.922 0.107 -0.484 21 | ATOM 10 H09 MOL 1 -0.923 1.892 -0.483 22 | TER 23 | CONECT 1 2 24 | CONECT 2 3 25 | CONECT 3 4 26 | CONECT 3 5 27 | CONECT 1 6 28 | CONECT 1 7 29 | CONECT 1 8 30 | CONECT 2 9 31 | CONECT 2 10 32 | END 33 | -------------------------------------------------------------------------------- /Solvents/dimethylsulfoxide/dimethylsulfoxide.pdb: -------------------------------------------------------------------------------- 1 | TITLE dimethylsulfoxide 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 S01 MOL 1 -0.809 1.000 0.000 14 | ATOM 3 C02 MOL 1 -0.989 1.000 1.800 15 | ATOM 4 O03 MOL 1 -1.260 2.341 -0.498 16 | ATOM 5 H04 MOL 1 1.364 0.085 0.473 17 | ATOM 6 H05 MOL 1 1.373 1.874 0.539 18 | ATOM 7 H06 MOL 1 1.348 1.034 -1.035 19 | ATOM 8 H07 MOL 1 -0.554 0.085 2.209 20 | ATOM 9 H08 MOL 1 -2.054 1.034 2.043 21 | ATOM 10 H09 MOL 1 -0.490 1.874 2.225 22 | TER 23 | CONECT 1 2 24 | CONECT 2 3 25 | CONECT 2 4 26 | CONECT 1 5 27 | CONECT 1 6 28 | CONECT 1 7 29 | CONECT 3 8 30 | CONECT 3 9 31 | CONECT 3 10 32 | END 33 | -------------------------------------------------------------------------------- /Solvents/methylacetate/methylacetate.pdb: -------------------------------------------------------------------------------- 1 | TITLE methylacetate 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 O01 MOL 1 -0.428 1.000 0.000 14 | ATOM 3 C02 MOL 1 -0.980 1.000 1.243 15 | ATOM 4 C03 MOL 1 -2.476 1.002 1.161 16 | ATOM 5 O04 MOL 1 -0.354 1.000 2.295 17 | ATOM 6 H05 MOL 1 1.338 0.999 -1.040 18 | ATOM 7 H06 MOL 1 1.382 0.099 0.490 19 | ATOM 8 H07 MOL 1 1.382 1.902 0.487 20 | ATOM 9 H08 MOL 1 -2.810 1.003 0.119 21 | ATOM 10 H09 MOL 1 -2.862 1.901 1.648 22 | ATOM 11 H0A MOL 1 -2.864 0.103 1.647 23 | TER 24 | CONECT 1 2 25 | CONECT 2 3 26 | CONECT 3 4 27 | CONECT 3 5 28 | CONECT 1 6 29 | CONECT 1 7 30 | CONECT 1 8 31 | CONECT 4 9 32 | CONECT 4 10 33 | CONECT 4 11 34 | END 35 | -------------------------------------------------------------------------------- /Solvents/1-bromopropane/1-bromopropane.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1-bromopropane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.520 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.069 1.000 1.416 15 | ATOM 4 Br3 MOL 1 -3.015 1.002 1.366 16 | ATOM 5 H04 MOL 1 1.379 0.999 -1.027 17 | ATOM 6 H05 MOL 1 1.391 0.112 0.508 18 | ATOM 7 H06 MOL 1 1.391 1.889 0.505 19 | ATOM 8 H07 MOL 1 -0.878 0.119 -0.547 20 | ATOM 9 H08 MOL 1 -0.878 1.881 -0.547 21 | ATOM 10 H09 MOL 1 -0.769 1.893 1.971 22 | ATOM 11 H0A MOL 1 -0.771 0.106 1.970 23 | TER 24 | CONECT 1 2 25 | CONECT 2 3 26 | CONECT 3 4 27 | CONECT 1 5 28 | CONECT 1 6 29 | CONECT 1 7 30 | CONECT 2 8 31 | CONECT 2 9 32 | CONECT 3 10 33 | CONECT 3 11 34 | END 35 | -------------------------------------------------------------------------------- /Solvents/pyridine/pyridine.pdb: -------------------------------------------------------------------------------- 1 | TITLE pyridine 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.391 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.045 1.000 1.222 15 | ATOM 4 N03 MOL 1 -0.409 1.000 2.413 16 | ATOM 5 C04 MOL 1 0.941 1.000 2.377 17 | ATOM 6 C05 MOL 1 1.681 1.000 1.213 18 | ATOM 7 H06 MOL 1 1.548 0.999 -0.938 19 | ATOM 8 H07 MOL 1 -0.951 1.001 -0.928 20 | ATOM 9 H08 MOL 1 -2.130 0.999 1.274 21 | ATOM 10 H09 MOL 1 1.429 1.001 3.348 22 | ATOM 11 H0A MOL 1 2.764 0.999 1.247 23 | TER 24 | CONECT 1 2 25 | CONECT 2 3 26 | CONECT 3 4 27 | CONECT 4 5 28 | CONECT 1 6 29 | CONECT 1 7 30 | CONECT 2 8 31 | CONECT 3 9 32 | CONECT 5 10 33 | CONECT 6 11 34 | CONECT 5 6 35 | END 36 | -------------------------------------------------------------------------------- /Solvents/1,3-dichloropropane/1,3-dichloropropane.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1,3-dichloropropane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 Cl0 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.778 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.309 1.000 1.426 15 | ATOM 4 C03 MOL 1 -2.831 0.998 1.424 16 | ATOM 5 Cl1 MOL 1 -3.453 0.996 3.089 17 | ATOM 6 H05 MOL 1 -1.109 0.111 -0.546 18 | ATOM 7 H06 MOL 1 -1.109 1.889 -0.546 19 | ATOM 8 H07 MOL 1 -0.939 1.884 1.960 20 | ATOM 9 H08 MOL 1 -0.937 0.117 1.959 21 | ATOM 10 H09 MOL 1 -3.224 0.109 0.922 22 | ATOM 11 H0A MOL 1 -3.225 1.887 0.923 23 | TER 24 | CONECT 1 2 25 | CONECT 2 3 26 | CONECT 3 4 27 | CONECT 4 5 28 | CONECT 2 6 29 | CONECT 2 7 30 | CONECT 3 8 31 | CONECT 3 9 32 | CONECT 4 10 33 | CONECT 4 11 34 | END 35 | -------------------------------------------------------------------------------- /Solvents/benzene/benzene.pdb: -------------------------------------------------------------------------------- 1 | TITLE benzene 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.395 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.091 1.000 1.209 15 | ATOM 4 C03 MOL 1 -0.392 1.000 2.415 16 | ATOM 5 C04 MOL 1 1.003 1.000 2.412 17 | ATOM 6 C05 MOL 1 1.696 1.000 1.209 18 | ATOM 7 H06 MOL 1 1.543 1.001 -0.942 19 | ATOM 8 H07 MOL 1 -0.937 0.999 -0.942 20 | ATOM 9 H08 MOL 1 -2.178 1.001 1.209 21 | ATOM 10 H09 MOL 1 -0.934 1.001 3.357 22 | ATOM 11 H0A MOL 1 1.548 0.999 3.352 23 | ATOM 12 H0B MOL 1 2.783 1.001 1.209 24 | TER 25 | CONECT 1 2 26 | CONECT 2 3 27 | CONECT 3 4 28 | CONECT 4 5 29 | CONECT 1 6 30 | CONECT 1 7 31 | CONECT 2 8 32 | CONECT 3 9 33 | CONECT 4 10 34 | CONECT 5 11 35 | CONECT 6 12 36 | CONECT 5 6 37 | END 38 | -------------------------------------------------------------------------------- /Solvents/N-methylacetamide/N-methylacetamide.pdb: -------------------------------------------------------------------------------- 1 | TITLE N-methylacetamide 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 N01 MOL 1 -0.440 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.147 1.000 1.179 15 | ATOM 4 C03 MOL 1 -2.643 1.002 1.006 16 | ATOM 5 O04 MOL 1 -0.619 1.000 2.286 17 | ATOM 6 H05 MOL 1 1.351 0.999 -1.034 18 | ATOM 7 H06 MOL 1 1.361 0.108 0.518 19 | ATOM 8 H07 MOL 1 1.361 1.894 0.516 20 | ATOM 9 H08 MOL 1 -0.929 1.001 -0.885 21 | ATOM 10 H09 MOL 1 -2.930 1.003 -0.049 22 | ATOM 11 H0A MOL 1 -3.054 1.897 1.480 23 | ATOM 12 H0B MOL 1 -3.056 0.107 1.479 24 | TER 25 | CONECT 1 2 26 | CONECT 2 3 27 | CONECT 3 4 28 | CONECT 3 5 29 | CONECT 1 6 30 | CONECT 1 7 31 | CONECT 1 8 32 | CONECT 2 9 33 | CONECT 4 10 34 | CONECT 4 11 35 | CONECT 4 12 36 | END 37 | -------------------------------------------------------------------------------- /Solvents/bromobenzene/bromobenzene.pdb: -------------------------------------------------------------------------------- 1 | TITLE bromobenzene 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 Br0 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.891 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.581 1.000 1.211 15 | ATOM 4 C03 MOL 1 -2.977 0.998 1.210 16 | ATOM 5 C04 MOL 1 -3.672 0.997 0.000 17 | ATOM 6 C05 MOL 1 -2.972 0.997 -1.207 18 | ATOM 7 C06 MOL 1 -1.581 0.998 -1.211 19 | ATOM 8 H07 MOL 1 -1.044 1.000 2.156 20 | ATOM 9 H08 MOL 1 -3.521 1.000 2.151 21 | ATOM 10 H09 MOL 1 -4.760 0.995 0.000 22 | ATOM 11 H0A MOL 1 -3.515 0.997 -2.149 23 | ATOM 12 H0B MOL 1 -1.044 0.997 -2.156 24 | TER 25 | CONECT 1 2 26 | CONECT 2 3 27 | CONECT 3 4 28 | CONECT 4 5 29 | CONECT 5 6 30 | CONECT 2 7 31 | CONECT 3 8 32 | CONECT 4 9 33 | CONECT 5 10 34 | CONECT 6 11 35 | CONECT 7 12 36 | CONECT 6 7 37 | END 38 | -------------------------------------------------------------------------------- /Solvents/fluorobenzene/fluorobenzene.pdb: -------------------------------------------------------------------------------- 1 | TITLE fluorobenzene 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 F00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.340 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.023 1.000 1.211 15 | ATOM 4 C03 MOL 1 -2.417 1.002 1.211 16 | ATOM 5 C04 MOL 1 -3.112 1.003 -0.001 17 | ATOM 6 C05 MOL 1 -2.413 1.003 -1.210 18 | ATOM 7 C06 MOL 1 -1.023 1.002 -1.211 19 | ATOM 8 H07 MOL 1 -0.465 0.998 2.142 20 | ATOM 9 H08 MOL 1 -2.961 1.003 2.152 21 | ATOM 10 H09 MOL 1 -4.199 1.003 -0.002 22 | ATOM 11 H0A MOL 1 -2.956 1.005 -2.152 23 | ATOM 12 H0B MOL 1 -0.465 1.000 -2.142 24 | TER 25 | CONECT 1 2 26 | CONECT 2 3 27 | CONECT 3 4 28 | CONECT 4 5 29 | CONECT 5 6 30 | CONECT 2 7 31 | CONECT 3 8 32 | CONECT 4 9 33 | CONECT 5 10 34 | CONECT 6 11 35 | CONECT 7 12 36 | CONECT 6 7 37 | END 38 | -------------------------------------------------------------------------------- /Solvents/N,N-dimethylformamide/N,N-dimethylformamide.pdb: -------------------------------------------------------------------------------- 1 | TITLE N,N-dimethylformamide 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 N01 MOL 1 -0.447 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.177 1.000 1.252 15 | ATOM 4 C03 MOL 1 -1.147 1.002 -1.189 16 | ATOM 5 O04 MOL 1 -2.366 1.003 -1.297 17 | ATOM 6 H05 MOL 1 1.398 1.000 1.018 18 | ATOM 7 H06 MOL 1 1.352 1.889 -0.533 19 | ATOM 8 H07 MOL 1 1.352 0.111 -0.533 20 | ATOM 9 H08 MOL 1 -0.496 1.000 2.107 21 | ATOM 10 H09 MOL 1 -1.813 0.111 1.291 22 | ATOM 11 H0A MOL 1 -1.813 1.889 1.291 23 | ATOM 12 H0B MOL 1 -0.485 1.003 -2.071 24 | TER 25 | CONECT 1 2 26 | CONECT 2 3 27 | CONECT 2 4 28 | CONECT 4 5 29 | CONECT 1 6 30 | CONECT 1 7 31 | CONECT 1 8 32 | CONECT 3 9 33 | CONECT 3 10 34 | CONECT 3 11 35 | CONECT 4 12 36 | END 37 | -------------------------------------------------------------------------------- /GAML/scripts/bash_genTopfiles.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # version 0.10: start 4 | # version 0.20: more powerful 5 | 6 | CHARGEPATH='' 7 | TOPPATH=topol.top 8 | 9 | if [[ -f settingfile-pair.txt ]] 10 | then 11 | FILE=settingfile-pair.txt 12 | elif [[ -f GAML_settingfile-training-sel.txt ]] 13 | then 14 | FILE=GAML_settingfile-training-sel.txt 15 | else 16 | echo "Error: no symmetry_list is defined" 17 | exit 1 18 | fi 19 | 20 | 21 | 22 | # 23 | # END of user inputs 24 | # 25 | 26 | symmetry_list=$(grep 'symmetry_list' $FILE | head -n 1) 27 | symmetry_list=${symmetry_list##*=} 28 | 29 | nm=${CHARGEPATH#*_} 30 | nm=${nm//\.*} 31 | TOPFOLDER=Topfile_$nm 32 | 33 | if [[ ! -f $CHARGEPATH ]]; then { echo "Error: no charge file"; exit 1; } fi 34 | if [[ ! -f $TOPPATH ]]; then { echo "Error: no top file"; exit 1; } fi 35 | if [[ -z $symmetry_list ]]; then { echo "Error: no symmetry_list"; exit 1; } fi 36 | if [[ -d $TOPFOLDER ]]; then { echo "Error: top folder already exist"; exit 1; } fi 37 | 38 | 39 | SETTINGFILE="#GAML-DES 40 | command = file_gen_gromacstop 41 | toppath = $TOPPATH 42 | charge_path = $CHARGEPATH 43 | symmetry_list = $symmetry_list 44 | reschoose = 45 | fname = top 46 | gennm = # default is None 47 | in_keyword = PAIR 48 | cut_keyword = # default is MAE 49 | " 50 | 51 | mkdir $TOPFOLDER 52 | cd $TOPFOLDER 53 | cp ../$CHARGEPATH ../$TOPPATH . 54 | echo "$SETTINGFILE" > settingfile.txt 55 | echo y | gaml settingfile.txt 56 | 57 | echo "DONE everything" 58 | -------------------------------------------------------------------------------- /Solvents/1-propanamine/1-propanamine.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1-propanamine 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.521 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.075 1.000 1.422 15 | ATOM 4 N03 MOL 1 -2.533 0.998 1.396 16 | ATOM 5 H04 MOL 1 1.378 0.999 -1.027 17 | ATOM 6 H05 MOL 1 1.391 0.112 0.507 18 | ATOM 7 H06 MOL 1 1.391 1.889 0.505 19 | ATOM 8 H07 MOL 1 -0.878 0.116 -0.543 20 | ATOM 9 H08 MOL 1 -0.877 1.884 -0.544 21 | ATOM 10 H09 MOL 1 -0.723 1.884 1.966 22 | ATOM 11 H0A MOL 1 -0.727 0.113 1.962 23 | ATOM 12 H0B MOL 1 -2.869 1.835 0.920 24 | ATOM 13 H0C MOL 1 -2.887 1.051 2.350 25 | TER 26 | CONECT 1 2 27 | CONECT 2 3 28 | CONECT 3 4 29 | CONECT 1 5 30 | CONECT 1 6 31 | CONECT 1 7 32 | CONECT 2 8 33 | CONECT 2 9 34 | CONECT 3 10 35 | CONECT 3 11 36 | CONECT 4 12 37 | CONECT 4 13 38 | END 39 | -------------------------------------------------------------------------------- /Solvents/1-nitropropane/1-nitropropane.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1-nitropropane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.520 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.068 1.000 1.419 15 | ATOM 4 N03 MOL 1 -2.565 0.998 1.348 16 | ATOM 5 O04 MOL 1 -3.128 2.100 1.325 17 | ATOM 6 O05 MOL 1 -3.125 -0.105 1.315 18 | ATOM 7 H06 MOL 1 1.379 1.001 -1.027 19 | ATOM 8 H07 MOL 1 1.391 0.111 0.505 20 | ATOM 9 H08 MOL 1 1.391 1.888 0.508 21 | ATOM 10 H09 MOL 1 -0.879 0.119 -0.547 22 | ATOM 11 H0A MOL 1 -0.879 1.881 -0.547 23 | ATOM 12 H0B MOL 1 -0.770 1.893 1.979 24 | ATOM 13 H0C MOL 1 -0.769 0.108 1.979 25 | TER 26 | CONECT 1 2 27 | CONECT 2 3 28 | CONECT 3 4 29 | CONECT 4 5 30 | CONECT 4 6 31 | CONECT 1 7 32 | CONECT 1 8 33 | CONECT 1 9 34 | CONECT 2 10 35 | CONECT 2 11 36 | CONECT 3 12 37 | CONECT 3 13 38 | END 39 | -------------------------------------------------------------------------------- /Solvents/2-nitropropane/2-nitropropane.pdb: -------------------------------------------------------------------------------- 1 | TITLE 2-nitropropane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.521 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.117 1.000 1.400 15 | ATOM 4 N03 MOL 1 -1.005 2.231 -0.730 16 | ATOM 5 O04 MOL 1 -0.685 3.337 -0.275 17 | ATOM 6 O05 MOL 1 -1.695 2.042 -1.741 18 | ATOM 7 H06 MOL 1 1.381 0.089 0.473 19 | ATOM 8 H07 MOL 1 1.409 1.856 0.548 20 | ATOM 9 H08 MOL 1 1.393 1.038 -1.022 21 | ATOM 10 H09 MOL 1 -0.891 0.134 -0.561 22 | ATOM 11 H0A MOL 1 -0.792 1.868 1.984 23 | ATOM 12 H0B MOL 1 -0.813 0.100 1.945 24 | ATOM 13 H0C MOL 1 -2.212 1.018 1.360 25 | TER 26 | CONECT 1 2 27 | CONECT 2 3 28 | CONECT 2 4 29 | CONECT 4 5 30 | CONECT 4 6 31 | CONECT 1 7 32 | CONECT 1 8 33 | CONECT 1 9 34 | CONECT 2 10 35 | CONECT 3 11 36 | CONECT 3 12 37 | CONECT 3 13 38 | END 39 | -------------------------------------------------------------------------------- /Solvents/phenol/phenol.pdb: -------------------------------------------------------------------------------- 1 | TITLE phenol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 O00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.364 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.088 1.000 1.189 15 | ATOM 4 C03 MOL 1 -2.483 0.998 1.140 16 | ATOM 5 C04 MOL 1 -3.140 0.997 -0.091 17 | ATOM 6 C05 MOL 1 -2.403 0.997 -1.276 18 | ATOM 7 C06 MOL 1 -1.011 0.998 -1.231 19 | ATOM 8 H07 MOL 1 1.307 1.000 0.921 20 | ATOM 9 H08 MOL 1 -0.588 1.002 2.152 21 | ATOM 10 H09 MOL 1 -3.058 0.997 2.063 22 | ATOM 11 H0A MOL 1 -4.227 0.997 -0.126 23 | ATOM 12 H0B MOL 1 -2.914 0.995 -2.235 24 | ATOM 13 H0C MOL 1 -0.430 0.997 -2.149 25 | TER 26 | CONECT 1 2 27 | CONECT 2 3 28 | CONECT 3 4 29 | CONECT 4 5 30 | CONECT 5 6 31 | CONECT 2 7 32 | CONECT 1 8 33 | CONECT 3 9 34 | CONECT 4 10 35 | CONECT 5 11 36 | CONECT 6 12 37 | CONECT 7 13 38 | CONECT 6 7 39 | END 40 | -------------------------------------------------------------------------------- /Solvents/benzenthiol/benzenthiol.pdb: -------------------------------------------------------------------------------- 1 | TITLE benzenthiol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 S00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.780 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.504 1.000 1.197 15 | ATOM 4 C03 MOL 1 -2.900 1.002 1.174 16 | ATOM 5 C04 MOL 1 -3.578 1.003 -0.044 17 | ATOM 6 C05 MOL 1 -2.860 1.003 -1.239 18 | ATOM 7 C06 MOL 1 -1.466 1.002 -1.219 19 | ATOM 8 H07 MOL 1 1.172 0.822 1.317 20 | ATOM 9 H08 MOL 1 -0.993 1.000 2.156 21 | ATOM 10 H09 MOL 1 -3.457 1.003 2.107 22 | ATOM 11 H0A MOL 1 -4.665 1.005 -0.062 23 | ATOM 12 H0B MOL 1 -3.386 1.005 -2.190 24 | ATOM 13 H0C MOL 1 -0.918 1.000 -2.158 25 | TER 26 | CONECT 1 2 27 | CONECT 2 3 28 | CONECT 3 4 29 | CONECT 4 5 30 | CONECT 5 6 31 | CONECT 2 7 32 | CONECT 1 8 33 | CONECT 3 9 34 | CONECT 4 10 35 | CONECT 5 11 36 | CONECT 6 12 37 | CONECT 7 13 38 | CONECT 6 7 39 | END 40 | -------------------------------------------------------------------------------- /Solvents/benzonitrile/benzonitrile.pdb: -------------------------------------------------------------------------------- 1 | TITLE benzonitrile 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 N00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.161 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.594 1.000 0.002 15 | ATOM 4 C03 MOL 1 -2.296 2.205 0.116 16 | ATOM 5 C04 MOL 1 -3.692 2.204 0.119 17 | ATOM 6 C05 MOL 1 -4.387 0.999 0.008 18 | ATOM 7 C06 MOL 1 -3.689 -0.203 -0.106 19 | ATOM 8 C07 MOL 1 -2.296 -0.206 -0.109 20 | ATOM 9 H08 MOL 1 -1.761 3.149 0.204 21 | ATOM 10 H09 MOL 1 -4.237 3.140 0.209 22 | ATOM 11 H0A MOL 1 -5.474 0.999 0.012 23 | ATOM 12 H0B MOL 1 -4.234 -1.140 -0.191 24 | ATOM 13 H0C MOL 1 -1.761 -1.149 -0.197 25 | TER 26 | CONECT 1 2 27 | CONECT 2 3 28 | CONECT 3 4 29 | CONECT 4 5 30 | CONECT 5 6 31 | CONECT 6 7 32 | CONECT 3 8 33 | CONECT 4 9 34 | CONECT 5 10 35 | CONECT 6 11 36 | CONECT 7 12 37 | CONECT 8 13 38 | CONECT 7 8 39 | END 40 | -------------------------------------------------------------------------------- /Solvents/tetrahydrofuran/tetrahydrofuran.pdb: -------------------------------------------------------------------------------- 1 | TITLE tetrahydrofuran 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.507 1.000 0.000 14 | ATOM 3 C02 MOL 1 -0.816 1.000 1.481 15 | ATOM 4 O03 MOL 1 0.242 0.274 2.121 16 | ATOM 5 C04 MOL 1 1.314 0.112 1.185 17 | ATOM 6 H05 MOL 1 1.370 2.015 0.187 18 | ATOM 7 H06 MOL 1 1.441 0.639 -0.933 19 | ATOM 8 H07 MOL 1 -0.877 0.076 -0.460 20 | ATOM 9 H08 MOL 1 -0.947 1.850 -0.529 21 | ATOM 10 H09 MOL 1 -1.778 0.532 1.711 22 | ATOM 11 H0A MOL 1 -0.815 2.018 1.886 23 | ATOM 12 H0B MOL 1 1.344 -0.943 0.892 24 | ATOM 13 H0C MOL 1 2.263 0.371 1.663 25 | TER 26 | CONECT 1 2 27 | CONECT 2 3 28 | CONECT 3 4 29 | CONECT 1 5 30 | CONECT 1 6 31 | CONECT 1 7 32 | CONECT 2 8 33 | CONECT 2 9 34 | CONECT 3 10 35 | CONECT 3 11 36 | CONECT 5 12 37 | CONECT 5 13 38 | CONECT 4 5 39 | END 40 | -------------------------------------------------------------------------------- /Solvents/ethylacetate/ethylacetate.pdb: -------------------------------------------------------------------------------- 1 | TITLE ethylacetate 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.517 1.000 0.000 14 | ATOM 3 O02 MOL 1 -1.014 1.000 1.346 15 | ATOM 4 C03 MOL 1 -1.117 -0.221 1.937 16 | ATOM 5 C04 MOL 1 -1.646 -0.092 3.333 17 | ATOM 6 O05 MOL 1 -0.821 -1.289 1.418 18 | ATOM 7 H06 MOL 1 1.387 1.047 -1.022 19 | ATOM 8 H07 MOL 1 1.393 0.099 0.481 20 | ATOM 9 H08 MOL 1 1.383 1.857 0.563 21 | ATOM 10 H09 MOL 1 -0.919 0.155 -0.570 22 | ATOM 11 H0A MOL 1 -0.883 1.915 -0.476 23 | ATOM 12 H0B MOL 1 -1.899 0.948 3.560 24 | ATOM 13 H0C MOL 1 -0.884 -0.428 4.039 25 | ATOM 14 H0D MOL 1 -2.553 -0.694 3.430 26 | TER 27 | CONECT 1 2 28 | CONECT 2 3 29 | CONECT 3 4 30 | CONECT 4 5 31 | CONECT 4 6 32 | CONECT 1 7 33 | CONECT 1 8 34 | CONECT 1 9 35 | CONECT 2 10 36 | CONECT 2 11 37 | CONECT 5 12 38 | CONECT 5 13 39 | CONECT 5 14 40 | END 41 | -------------------------------------------------------------------------------- /Solvents/1-bromobutane/1-bromobutane.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1-bromobutane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.520 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.080 1.000 1.422 15 | ATOM 4 C03 MOL 1 -2.599 1.002 1.409 16 | ATOM 5 Br4 MOL 1 -3.274 0.999 3.235 17 | ATOM 6 H05 MOL 1 1.378 0.999 -1.027 18 | ATOM 7 H06 MOL 1 1.391 0.112 0.508 19 | ATOM 8 H07 MOL 1 1.391 1.889 0.505 20 | ATOM 9 H08 MOL 1 -0.879 0.117 -0.541 21 | ATOM 10 H09 MOL 1 -0.879 1.883 -0.541 22 | ATOM 11 H0A MOL 1 -0.708 1.880 1.961 23 | ATOM 12 H0B MOL 1 -0.710 0.118 1.961 24 | ATOM 13 H0C MOL 1 -3.005 0.109 0.925 25 | ATOM 14 H0D MOL 1 -3.003 1.897 0.928 26 | TER 27 | CONECT 1 2 28 | CONECT 2 3 29 | CONECT 3 4 30 | CONECT 4 5 31 | CONECT 1 6 32 | CONECT 1 7 33 | CONECT 1 8 34 | CONECT 2 9 35 | CONECT 2 10 36 | CONECT 3 11 37 | CONECT 3 12 38 | CONECT 4 13 39 | CONECT 4 14 40 | END 41 | -------------------------------------------------------------------------------- /Solvents/1-chlorobutane/1-chlorobutane.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1-chlorobutane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.520 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.080 1.000 1.422 15 | ATOM 4 C03 MOL 1 -2.603 0.998 1.411 16 | ATOM 5 Cl0 MOL 1 -3.235 0.996 3.074 17 | ATOM 6 H05 MOL 1 1.378 0.999 -1.027 18 | ATOM 7 H06 MOL 1 1.391 0.112 0.508 19 | ATOM 8 H07 MOL 1 1.391 1.889 0.505 20 | ATOM 9 H08 MOL 1 -0.879 0.117 -0.541 21 | ATOM 10 H09 MOL 1 -0.879 1.883 -0.541 22 | ATOM 11 H0A MOL 1 -0.713 1.884 1.959 23 | ATOM 12 H0B MOL 1 -0.711 0.118 1.960 24 | ATOM 13 H0C MOL 1 -2.993 0.109 0.906 25 | ATOM 14 H0D MOL 1 -2.995 1.887 0.907 26 | TER 27 | CONECT 1 2 28 | CONECT 2 3 29 | CONECT 3 4 30 | CONECT 4 5 31 | CONECT 1 6 32 | CONECT 1 7 33 | CONECT 1 8 34 | CONECT 2 9 35 | CONECT 2 10 36 | CONECT 3 11 37 | CONECT 3 12 38 | CONECT 4 13 39 | CONECT 4 14 40 | END 41 | -------------------------------------------------------------------------------- /Solvents/aniline/aniline.pdb: -------------------------------------------------------------------------------- 1 | TITLE aniline 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 N00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.401 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.104 1.000 1.207 15 | ATOM 4 C03 MOL 1 -2.496 1.121 1.222 16 | ATOM 5 C04 MOL 1 -3.191 1.298 0.028 17 | ATOM 6 C05 MOL 1 -2.492 1.352 -1.176 18 | ATOM 7 C06 MOL 1 -1.104 1.236 -1.184 19 | ATOM 8 H07 MOL 1 1.404 0.528 0.803 20 | ATOM 9 H08 MOL 1 1.403 0.682 -0.876 21 | ATOM 10 H09 MOL 1 -0.571 0.904 2.149 22 | ATOM 11 H0A MOL 1 -3.033 1.079 2.165 23 | ATOM 12 H0B MOL 1 -4.273 1.394 0.037 24 | ATOM 13 H0C MOL 1 -3.029 1.486 -2.111 25 | ATOM 14 H0D MOL 1 -0.571 1.329 -2.126 26 | TER 27 | CONECT 1 2 28 | CONECT 2 3 29 | CONECT 3 4 30 | CONECT 4 5 31 | CONECT 5 6 32 | CONECT 2 7 33 | CONECT 1 8 34 | CONECT 1 9 35 | CONECT 3 10 36 | CONECT 4 11 37 | CONECT 5 12 38 | CONECT 6 13 39 | CONECT 7 14 40 | CONECT 6 7 41 | END 42 | -------------------------------------------------------------------------------- /Solvents/1,4-dichlorobutane/1,4-dichlorobutane.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1,4-dichlorobutane 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 Cl0 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.778 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.306 1.000 1.429 15 | ATOM 4 C03 MOL 1 -2.835 0.998 1.452 16 | ATOM 5 C04 MOL 1 -3.361 1.000 2.881 17 | ATOM 6 Cl1 MOL 1 -5.139 0.996 2.882 18 | ATOM 7 H06 MOL 1 -1.110 0.111 -0.545 19 | ATOM 8 H07 MOL 1 -1.110 1.890 -0.544 20 | ATOM 9 H08 MOL 1 -0.934 1.884 1.962 21 | ATOM 10 H09 MOL 1 -0.932 0.117 1.962 22 | ATOM 11 H0A MOL 1 -3.206 0.114 0.920 23 | ATOM 12 H0B MOL 1 -3.209 1.880 0.917 24 | ATOM 13 H0C MOL 1 -3.030 1.891 3.423 25 | ATOM 14 H0D MOL 1 -3.026 0.113 3.427 26 | TER 27 | CONECT 1 2 28 | CONECT 2 3 29 | CONECT 3 4 30 | CONECT 4 5 31 | CONECT 5 6 32 | CONECT 2 7 33 | CONECT 2 8 34 | CONECT 3 9 35 | CONECT 3 10 36 | CONECT 4 11 37 | CONECT 4 12 38 | CONECT 5 13 39 | CONECT 5 14 40 | END 41 | -------------------------------------------------------------------------------- /Solvents/nitrobenzene/nitrobenzene.pdb: -------------------------------------------------------------------------------- 1 | TITLE nitrobenzene 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 O00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 N01 MOL 1 -0.240 1.000 0.000 14 | ATOM 3 O02 MOL 1 -0.940 1.000 1.023 15 | ATOM 4 C03 MOL 1 -0.923 1.002 -1.299 16 | ATOM 5 C04 MOL 1 -0.166 1.003 -2.479 17 | ATOM 6 C05 MOL 1 -0.822 1.006 -3.712 18 | ATOM 7 C06 MOL 1 -2.217 1.008 -3.761 19 | ATOM 8 C07 MOL 1 -2.963 1.006 -2.581 20 | ATOM 9 C08 MOL 1 -2.323 1.003 -1.346 21 | ATOM 10 H09 MOL 1 0.921 1.003 -2.455 22 | ATOM 11 H0A MOL 1 -0.244 1.009 -4.634 23 | ATOM 12 H0B MOL 1 -2.723 1.011 -4.725 24 | ATOM 13 H0C MOL 1 -4.050 1.009 -2.627 25 | ATOM 14 H0D MOL 1 -2.919 1.003 -0.435 26 | TER 27 | CONECT 1 2 28 | CONECT 2 3 29 | CONECT 2 4 30 | CONECT 4 5 31 | CONECT 5 6 32 | CONECT 6 7 33 | CONECT 7 8 34 | CONECT 4 9 35 | CONECT 5 10 36 | CONECT 6 11 37 | CONECT 7 12 38 | CONECT 8 13 39 | CONECT 9 14 40 | CONECT 8 9 41 | END 42 | -------------------------------------------------------------------------------- /Solvents/cyclopentanone/cyclopentanone.pdb: -------------------------------------------------------------------------------- 1 | TITLE cyclopentanone 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 O00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.227 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.059 1.000 1.250 15 | ATOM 4 C03 MOL 1 -2.406 0.542 0.712 16 | ATOM 5 C04 MOL 1 -2.480 1.111 -0.699 17 | ATOM 6 C05 MOL 1 -1.062 1.057 -1.249 18 | ATOM 7 H06 MOL 1 -1.108 2.020 1.641 19 | ATOM 8 H07 MOL 1 -0.662 0.312 1.999 20 | ATOM 9 H08 MOL 1 -3.235 0.885 1.339 21 | ATOM 10 H09 MOL 1 -2.441 -0.554 0.675 22 | ATOM 11 H0A MOL 1 -2.827 2.151 -0.666 23 | ATOM 12 H0B MOL 1 -3.176 0.548 -1.329 24 | ATOM 13 H0C MOL 1 -0.826 1.954 -1.828 25 | ATOM 14 H0D MOL 1 -0.892 0.154 -1.841 26 | TER 27 | CONECT 1 2 28 | CONECT 2 3 29 | CONECT 3 4 30 | CONECT 4 5 31 | CONECT 2 6 32 | CONECT 3 7 33 | CONECT 3 8 34 | CONECT 4 9 35 | CONECT 4 10 36 | CONECT 5 11 37 | CONECT 5 12 38 | CONECT 6 13 39 | CONECT 6 14 40 | CONECT 5 6 41 | END 42 | -------------------------------------------------------------------------------- /Solvents/2-chloroaniline/2-chloroaniline.pdb: -------------------------------------------------------------------------------- 1 | TITLE 2-chloroaniline 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 N00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.408 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.086 1.000 1.225 15 | ATOM 4 C03 MOL 1 -2.478 1.121 1.273 16 | ATOM 5 C04 MOL 1 -3.206 1.298 0.098 17 | ATOM 6 C05 MOL 1 -2.541 1.353 -1.126 18 | ATOM 7 C06 MOL 1 -1.151 1.227 -1.173 19 | ATOM 8 Cl0 MOL 1 -0.360 1.354 -2.707 20 | ATOM 9 H08 MOL 1 1.414 0.481 0.767 21 | ATOM 10 H09 MOL 1 1.385 0.741 -0.906 22 | ATOM 11 H0A MOL 1 -0.531 0.906 2.155 23 | ATOM 12 H0B MOL 1 -2.990 1.079 2.231 24 | ATOM 13 H0C MOL 1 -4.288 1.393 0.138 25 | ATOM 14 H0D MOL 1 -3.110 1.496 -2.041 26 | TER 27 | CONECT 1 2 28 | CONECT 2 3 29 | CONECT 3 4 30 | CONECT 4 5 31 | CONECT 5 6 32 | CONECT 2 7 33 | CONECT 7 8 34 | CONECT 1 9 35 | CONECT 1 10 36 | CONECT 3 11 37 | CONECT 4 12 38 | CONECT 5 13 39 | CONECT 6 14 40 | CONECT 6 7 41 | END 42 | -------------------------------------------------------------------------------- /Solvents/3-methylpyridine/3-methylpyridine.pdb: -------------------------------------------------------------------------------- 1 | TITLE 3-methylpyridine 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.495 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.232 1.000 1.185 15 | ATOM 4 C03 MOL 1 -2.623 1.002 1.130 16 | ATOM 5 C04 MOL 1 -3.230 1.003 -0.115 17 | ATOM 6 N05 MOL 1 -2.549 1.003 -1.281 18 | ATOM 7 C06 MOL 1 -1.204 1.002 -1.197 19 | ATOM 8 H07 MOL 1 1.400 0.954 1.018 20 | ATOM 9 H08 MOL 1 1.377 1.914 -0.470 21 | ATOM 10 H09 MOL 1 1.378 0.130 -0.546 22 | ATOM 11 H0A MOL 1 -0.732 0.998 2.150 23 | ATOM 12 H0B MOL 1 -3.218 1.003 2.036 24 | ATOM 13 H0C MOL 1 -4.312 1.005 -0.209 25 | ATOM 14 H0D MOL 1 -0.688 1.003 -2.155 26 | TER 27 | CONECT 1 2 28 | CONECT 2 3 29 | CONECT 3 4 30 | CONECT 4 5 31 | CONECT 5 6 32 | CONECT 2 7 33 | CONECT 1 8 34 | CONECT 1 9 35 | CONECT 1 10 36 | CONECT 3 11 37 | CONECT 4 12 38 | CONECT 5 13 39 | CONECT 7 14 40 | CONECT 6 7 41 | END 42 | -------------------------------------------------------------------------------- /Solvents/4-methylpyridine/4-methylpyridine.pdb: -------------------------------------------------------------------------------- 1 | TITLE 4-methylpyridine 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.498 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.222 1.000 1.194 15 | ATOM 4 C03 MOL 1 -2.607 0.998 1.130 16 | ATOM 5 N04 MOL 1 -3.307 0.997 -0.025 17 | ATOM 6 C05 MOL 1 -2.585 0.997 -1.165 18 | ATOM 7 C06 MOL 1 -1.201 0.998 -1.207 19 | ATOM 8 H07 MOL 1 1.400 1.079 1.016 20 | ATOM 9 H08 MOL 1 1.378 1.852 -0.574 21 | ATOM 10 H09 MOL 1 1.376 0.071 -0.441 22 | ATOM 11 H0A MOL 1 -0.724 1.002 2.158 23 | ATOM 12 H0B MOL 1 -3.207 0.997 2.035 24 | ATOM 13 H0C MOL 1 -3.168 0.994 -2.081 25 | ATOM 14 H0D MOL 1 -0.683 0.997 -2.160 26 | TER 27 | CONECT 1 2 28 | CONECT 2 3 29 | CONECT 3 4 30 | CONECT 4 5 31 | CONECT 5 6 32 | CONECT 2 7 33 | CONECT 1 8 34 | CONECT 1 9 35 | CONECT 1 10 36 | CONECT 3 11 37 | CONECT 4 12 38 | CONECT 6 13 39 | CONECT 7 14 40 | CONECT 6 7 41 | END 42 | -------------------------------------------------------------------------------- /Solvents/1-cyclopropylethanone/1-cyclopropylethanone.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1-cyclopropylethanone 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.502 1.000 0.000 14 | ATOM 3 O02 MOL 1 -1.168 1.000 1.029 15 | ATOM 4 C03 MOL 1 -1.144 0.998 -1.347 16 | ATOM 5 C04 MOL 1 -2.456 0.283 -1.562 17 | ATOM 6 C05 MOL 1 -2.412 1.785 -1.576 18 | ATOM 7 H06 MOL 1 1.365 1.113 1.024 19 | ATOM 8 H07 MOL 1 1.370 1.838 -0.597 20 | ATOM 9 H08 MOL 1 1.366 0.055 -0.408 21 | ATOM 10 H09 MOL 1 -0.444 0.967 -2.177 22 | ATOM 11 H0A MOL 1 -2.928 -0.199 -0.712 23 | ATOM 12 H0B MOL 1 -2.608 -0.230 -2.504 24 | ATOM 13 H0C MOL 1 -2.855 2.307 -0.734 25 | ATOM 14 H0D MOL 1 -2.533 2.289 -2.528 26 | TER 27 | CONECT 1 2 28 | CONECT 2 3 29 | CONECT 2 4 30 | CONECT 4 5 31 | CONECT 4 6 32 | CONECT 1 7 33 | CONECT 1 8 34 | CONECT 1 9 35 | CONECT 4 10 36 | CONECT 5 11 37 | CONECT 5 12 38 | CONECT 6 13 39 | CONECT 6 14 40 | CONECT 5 6 41 | END 42 | -------------------------------------------------------------------------------- /Solvents/1-butanol/1-butanol.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1-butanol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.520 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.078 1.000 1.421 15 | ATOM 4 C03 MOL 1 -2.601 0.998 1.426 16 | ATOM 5 O04 MOL 1 -3.077 1.000 2.765 17 | ATOM 6 H05 MOL 1 1.378 0.999 -1.027 18 | ATOM 7 H06 MOL 1 1.391 0.112 0.508 19 | ATOM 8 H07 MOL 1 1.391 1.889 0.505 20 | ATOM 9 H08 MOL 1 -0.879 0.117 -0.541 21 | ATOM 10 H09 MOL 1 -0.879 1.883 -0.542 22 | ATOM 11 H0A MOL 1 -0.714 1.877 1.971 23 | ATOM 12 H0B MOL 1 -0.710 0.125 1.971 24 | ATOM 13 H0C MOL 1 -3.000 0.115 0.916 25 | ATOM 14 H0D MOL 1 -2.992 1.890 0.927 26 | ATOM 15 H0E MOL 1 -2.739 0.196 3.196 27 | TER 28 | CONECT 1 2 29 | CONECT 2 3 30 | CONECT 3 4 31 | CONECT 4 5 32 | CONECT 1 6 33 | CONECT 1 7 34 | CONECT 1 8 35 | CONECT 2 9 36 | CONECT 2 10 37 | CONECT 3 11 38 | CONECT 3 12 39 | CONECT 4 13 40 | CONECT 4 14 41 | CONECT 5 15 42 | END 43 | -------------------------------------------------------------------------------- /Solvents/diethylsulfide/diethylsulfide.pdb: -------------------------------------------------------------------------------- 1 | TITLE diethylsulfide 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.518 1.000 0.000 14 | ATOM 3 S02 MOL 1 -1.139 1.000 1.709 15 | ATOM 4 C03 MOL 1 -2.921 1.002 1.349 16 | ATOM 5 C04 MOL 1 -3.712 1.004 2.645 17 | ATOM 6 H05 MOL 1 1.372 1.001 -1.030 18 | ATOM 7 H06 MOL 1 1.401 0.109 0.495 19 | ATOM 8 H07 MOL 1 1.401 1.889 0.498 20 | ATOM 9 H08 MOL 1 -0.887 0.110 -0.518 21 | ATOM 10 H09 MOL 1 -0.887 1.890 -0.518 22 | ATOM 11 H0A MOL 1 -3.172 0.112 0.764 23 | ATOM 12 H0B MOL 1 -3.169 1.892 0.762 24 | ATOM 13 H0C MOL 1 -3.497 0.115 3.248 25 | ATOM 14 H0D MOL 1 -4.785 1.005 2.426 26 | ATOM 15 H0E MOL 1 -3.495 1.894 3.246 27 | TER 28 | CONECT 1 2 29 | CONECT 2 3 30 | CONECT 3 4 31 | CONECT 4 5 32 | CONECT 1 6 33 | CONECT 1 7 34 | CONECT 1 8 35 | CONECT 2 9 36 | CONECT 2 10 37 | CONECT 4 11 38 | CONECT 4 12 39 | CONECT 5 13 40 | CONECT 5 14 41 | CONECT 5 15 42 | END 43 | -------------------------------------------------------------------------------- /Solvents/n-butanethiol/n-butanethiol.pdb: -------------------------------------------------------------------------------- 1 | TITLE n-butanethiol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.520 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.079 1.000 1.424 15 | ATOM 4 C03 MOL 1 -2.605 0.998 1.409 16 | ATOM 5 S04 MOL 1 -3.261 1.000 3.103 17 | ATOM 6 H05 MOL 1 1.378 1.001 -1.027 18 | ATOM 7 H06 MOL 1 1.391 0.111 0.505 19 | ATOM 8 H07 MOL 1 1.391 1.888 0.508 20 | ATOM 9 H08 MOL 1 -0.879 0.117 -0.541 21 | ATOM 10 H09 MOL 1 -0.879 1.883 -0.541 22 | ATOM 11 H0A MOL 1 -0.708 1.886 1.956 23 | ATOM 12 H0B MOL 1 -0.706 0.116 1.956 24 | ATOM 13 H0C MOL 1 -2.985 0.112 0.892 25 | ATOM 14 H0D MOL 1 -2.986 1.884 0.892 26 | ATOM 15 H0E MOL 1 -2.729 -0.173 3.476 27 | TER 28 | CONECT 1 2 29 | CONECT 2 3 30 | CONECT 3 4 31 | CONECT 4 5 32 | CONECT 1 6 33 | CONECT 1 7 34 | CONECT 1 8 35 | CONECT 2 9 36 | CONECT 2 10 37 | CONECT 3 11 38 | CONECT 3 12 39 | CONECT 4 13 40 | CONECT 4 14 41 | CONECT 5 15 42 | END 43 | -------------------------------------------------------------------------------- /Solvents/pentanenitrile/pentanenitrile.pdb: -------------------------------------------------------------------------------- 1 | TITLE pentanenitrile 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.521 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.077 1.000 1.424 15 | ATOM 4 C03 MOL 1 -2.606 1.002 1.425 16 | ATOM 5 C04 MOL 1 -3.131 1.000 2.798 17 | ATOM 6 N05 MOL 1 -3.546 0.999 3.881 18 | ATOM 7 H06 MOL 1 1.379 1.001 -1.027 19 | ATOM 8 H07 MOL 1 1.391 0.111 0.505 20 | ATOM 9 H08 MOL 1 1.391 1.888 0.508 21 | ATOM 10 H09 MOL 1 -0.879 0.117 -0.541 22 | ATOM 11 H0A MOL 1 -0.879 1.883 -0.541 23 | ATOM 12 H0B MOL 1 -0.705 1.880 1.963 24 | ATOM 13 H0C MOL 1 -0.707 0.118 1.963 25 | ATOM 14 H0D MOL 1 -2.979 0.121 0.891 26 | ATOM 15 H0E MOL 1 -2.977 1.886 0.894 27 | TER 28 | CONECT 1 2 29 | CONECT 2 3 30 | CONECT 3 4 31 | CONECT 4 5 32 | CONECT 5 6 33 | CONECT 1 7 34 | CONECT 1 8 35 | CONECT 1 9 36 | CONECT 2 10 37 | CONECT 2 11 38 | CONECT 3 12 39 | CONECT 3 13 40 | CONECT 4 14 41 | CONECT 4 15 42 | END 43 | -------------------------------------------------------------------------------- /Solvents/toluene/toluene.pdb: -------------------------------------------------------------------------------- 1 | TITLE toluene 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.500 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.220 1.000 1.201 15 | ATOM 4 C03 MOL 1 -2.616 0.998 1.186 16 | ATOM 5 C04 MOL 1 -3.300 0.997 -0.028 17 | ATOM 6 C05 MOL 1 -2.589 0.997 -1.226 18 | ATOM 7 C06 MOL 1 -1.198 0.998 -1.214 19 | ATOM 8 H07 MOL 1 1.401 1.079 1.016 20 | ATOM 9 H08 MOL 1 1.378 1.852 -0.575 21 | ATOM 10 H09 MOL 1 1.375 0.071 -0.441 22 | ATOM 11 H0A MOL 1 -0.699 1.002 2.155 23 | ATOM 12 H0B MOL 1 -3.167 0.997 2.123 24 | ATOM 13 H0C MOL 1 -4.387 0.995 -0.039 25 | ATOM 14 H0D MOL 1 -3.122 0.995 -2.173 26 | ATOM 15 H0E MOL 1 -0.654 0.997 -2.157 27 | TER 28 | CONECT 1 2 29 | CONECT 2 3 30 | CONECT 3 4 31 | CONECT 4 5 32 | CONECT 5 6 33 | CONECT 2 7 34 | CONECT 1 8 35 | CONECT 1 9 36 | CONECT 1 10 37 | CONECT 3 11 38 | CONECT 4 12 39 | CONECT 5 13 40 | CONECT 6 14 41 | CONECT 7 15 42 | CONECT 6 7 43 | END 44 | -------------------------------------------------------------------------------- /Solvents/morpholine/morpholine.pdb: -------------------------------------------------------------------------------- 1 | TITLE morpholine 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.536 1.000 0.000 14 | ATOM 3 O02 MOL 1 -1.051 1.000 1.339 15 | ATOM 4 C03 MOL 1 -0.570 2.151 2.047 16 | ATOM 5 C04 MOL 1 0.965 2.173 2.087 17 | ATOM 6 N05 MOL 1 1.548 2.149 0.741 18 | ATOM 7 H06 MOL 1 1.367 1.029 -1.031 19 | ATOM 8 H07 MOL 1 1.364 0.073 0.460 20 | ATOM 9 H08 MOL 1 -0.906 0.098 -0.497 21 | ATOM 10 H09 MOL 1 -0.933 1.868 -0.540 22 | ATOM 11 H0A MOL 1 -0.967 2.101 3.066 23 | ATOM 12 H0B MOL 1 -0.970 3.057 1.576 24 | ATOM 13 H0C MOL 1 1.328 1.302 2.646 25 | ATOM 14 H0D MOL 1 1.306 3.073 2.609 26 | ATOM 15 H0E MOL 1 2.560 2.046 0.818 27 | TER 28 | CONECT 1 2 29 | CONECT 2 3 30 | CONECT 3 4 31 | CONECT 4 5 32 | CONECT 1 6 33 | CONECT 1 7 34 | CONECT 1 8 35 | CONECT 2 9 36 | CONECT 2 10 37 | CONECT 4 11 38 | CONECT 4 12 39 | CONECT 5 13 40 | CONECT 5 14 41 | CONECT 6 15 42 | CONECT 5 6 43 | END 44 | -------------------------------------------------------------------------------- /Solvents/tert-butylalcohol/tert-butylalcohol.pdb: -------------------------------------------------------------------------------- 1 | TITLE tert-butylalcohol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.528 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.072 1.000 1.428 15 | ATOM 4 C03 MOL 1 -1.064 2.199 -0.780 16 | ATOM 5 O04 MOL 1 -0.981 -0.183 -0.659 17 | ATOM 6 H05 MOL 1 1.402 1.897 0.482 18 | ATOM 7 H06 MOL 1 1.388 0.951 -1.024 19 | ATOM 8 H07 MOL 1 1.390 0.120 0.524 20 | ATOM 9 H08 MOL 1 -0.765 1.897 1.975 21 | ATOM 10 H09 MOL 1 -0.722 0.120 1.979 22 | ATOM 11 H0A MOL 1 -2.167 0.951 1.426 23 | ATOM 12 H0B MOL 1 -0.753 3.146 -0.328 24 | ATOM 13 H0C MOL 1 -2.160 2.177 -0.822 25 | ATOM 14 H0D MOL 1 -0.713 2.177 -1.818 26 | ATOM 15 H0E MOL 1 -0.642 -0.950 -0.165 27 | TER 28 | CONECT 1 2 29 | CONECT 2 3 30 | CONECT 2 4 31 | CONECT 2 5 32 | CONECT 1 6 33 | CONECT 1 7 34 | CONECT 1 8 35 | CONECT 3 9 36 | CONECT 3 10 37 | CONECT 3 11 38 | CONECT 4 12 39 | CONECT 4 13 40 | CONECT 4 14 41 | CONECT 5 15 42 | END 43 | -------------------------------------------------------------------------------- /Solvents/N,N-dimethylacetamide/N,N-dimethylacetamide.pdb: -------------------------------------------------------------------------------- 1 | TITLE N,N-dimethylacetamide 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.508 1.000 0.000 14 | ATOM 3 O02 MOL 1 -1.118 1.000 1.070 15 | ATOM 4 N03 MOL 1 -1.144 0.998 -1.233 16 | ATOM 5 C04 MOL 1 -0.469 0.997 -2.523 17 | ATOM 6 C05 MOL 1 -2.597 1.000 -1.275 18 | ATOM 7 H06 MOL 1 1.360 1.000 1.034 19 | ATOM 8 H07 MOL 1 1.377 1.901 -0.491 20 | ATOM 9 H08 MOL 1 1.377 0.099 -0.491 21 | ATOM 10 H09 MOL 1 0.617 0.997 -2.436 22 | ATOM 11 H0A MOL 1 -0.775 1.889 -3.077 23 | ATOM 12 H0B MOL 1 -0.775 0.103 -3.075 24 | ATOM 13 H0C MOL 1 -3.042 1.002 -0.277 25 | ATOM 14 H0D MOL 1 -2.934 0.105 -1.807 26 | ATOM 15 H0E MOL 1 -2.932 1.893 -1.811 27 | TER 28 | CONECT 1 2 29 | CONECT 2 3 30 | CONECT 2 4 31 | CONECT 4 5 32 | CONECT 4 6 33 | CONECT 1 7 34 | CONECT 1 8 35 | CONECT 1 9 36 | CONECT 5 10 37 | CONECT 5 11 38 | CONECT 5 12 39 | CONECT 6 13 40 | CONECT 6 14 41 | CONECT 6 15 42 | END 43 | -------------------------------------------------------------------------------- /Solvents/formaldehyde/formaldehyde.itp: -------------------------------------------------------------------------------- 1 | ; formaldehyde 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_802 H802 1.0080 0.348 A 2.50000E-01 1.25520E-01 18 | opls_800 C800 12.0110 -0.639 A 3.55000E-01 2.92880E-01 19 | opls_801 O801 15.9990 -0.057 A 2.96000E-01 8.78640E-01 20 | opls_803 H803 1.0080 0.000 A 2.50000E-01 1.25520E-01 21 | 22 | 23 | [ moleculetype ] 24 | ; name nrexcl 25 | MOL 3 26 | 27 | 28 | [ atoms ] 29 | ; nr type resnr residue atom cgnr charge mass 30 | 1 opls_800 1 MOL C00 1 -0.639 12.0110 31 | 2 opls_801 1 MOL O01 1 -0.057 15.9990 32 | 3 opls_802 1 MOL H02 1 0.348 1.0080 33 | 4 opls_802 1 MOL H03 1 0.348 1.0080 34 | 35 | 36 | [ bonds ] 37 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 38 | 2 1 1 0.1229 476976.000 39 | 3 1 1 0.1090 284512.000 40 | 4 1 1 0.1090 284512.000 41 | 42 | 43 | [ angles ] 44 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 45 | 2 1 3 1 123.000 292.880 46 | 2 1 4 1 123.000 292.880 47 | 3 1 4 1 115.000 292.880 48 | 49 | 50 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # -*- encoding: utf-8 -*- 3 | 4 | from setuptools import setup 5 | import os 6 | import GAML 7 | 8 | 9 | def read(*names): 10 | values = {} 11 | extensions = ['', '.txt', '.rst', '.md',] 12 | for name in names: 13 | v = '' 14 | for ext in extensions: 15 | filename = name + ext 16 | if os.path.isfile(filename): 17 | with open(filename) as f: 18 | v = f.read() 19 | values[name] = v 20 | return values 21 | 22 | 23 | long_description = """%(README)s""" % read('README') 24 | 25 | 26 | setup( 27 | name='GAML', 28 | version=GAML.__version__, 29 | description='Genetic Algorithm Machine Learning', 30 | long_description=long_description, 31 | long_description_content_type='text/markdown', 32 | classifiers=[ 33 | "Development Status :: 3 - Alpha", 34 | "Environment :: Console", 35 | "Intended Audience :: Developers", 36 | "Topic :: Software Development :: Build Tools", 37 | "Programming Language :: Python :: 3", 38 | "Topic :: Scientific/Engineering :: Chemistry", 39 | "Topic :: Scientific/Engineering :: Visualization", 40 | ], 41 | author='Orlando Acevedo', 42 | author_email='orlando.acevedo@miami.edu', 43 | keywords='Computational Chemistry Genetic Algorithm Machine Learning', 44 | maintainer='Xiang Zhong', 45 | maintainer_email='xxz385@miami.edu', 46 | url='https://github.com/orlandoacevedo/GAML', 47 | license='MIT', 48 | packages=['GAML'], 49 | package_data={'GAML':['scripts/*'],}, 50 | entry_points={ 51 | 'console_scripts': [ 52 | 'gaml = GAML.main:cmd_line_runner', 53 | ] 54 | }, 55 | install_requires=['matplotlib'], 56 | ) 57 | 58 | 59 | 60 | -------------------------------------------------------------------------------- /Solvents/1-butanamine/1-butanamine.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1-butanamine 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.520 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.080 1.000 1.423 15 | ATOM 4 C03 MOL 1 -2.608 1.002 1.415 16 | ATOM 5 N04 MOL 1 -3.120 1.004 2.780 17 | ATOM 6 H05 MOL 1 1.378 0.999 -1.027 18 | ATOM 7 H06 MOL 1 1.391 0.112 0.508 19 | ATOM 8 H07 MOL 1 1.391 1.889 0.505 20 | ATOM 9 H08 MOL 1 -0.879 0.117 -0.541 21 | ATOM 10 H09 MOL 1 -0.879 1.883 -0.542 22 | ATOM 11 H0A MOL 1 -0.711 1.883 1.960 23 | ATOM 12 H0B MOL 1 -0.711 0.116 1.959 24 | ATOM 13 H0C MOL 1 -2.985 0.119 0.887 25 | ATOM 14 H0D MOL 1 -2.980 1.890 0.893 26 | ATOM 15 H0E MOL 1 -2.802 0.166 3.266 27 | ATOM 16 H0F MOL 1 -4.138 0.951 2.759 28 | TER 29 | CONECT 1 2 30 | CONECT 2 3 31 | CONECT 3 4 32 | CONECT 4 5 33 | CONECT 1 6 34 | CONECT 1 7 35 | CONECT 1 8 36 | CONECT 2 9 37 | CONECT 2 10 38 | CONECT 3 11 39 | CONECT 3 12 40 | CONECT 4 13 41 | CONECT 4 14 42 | CONECT 5 15 43 | CONECT 5 16 44 | END 45 | -------------------------------------------------------------------------------- /Solvents/anisole/anisole.pdb: -------------------------------------------------------------------------------- 1 | TITLE anisole 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 O01 MOL 1 -0.424 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.003 1.000 1.240 15 | ATOM 4 C03 MOL 1 -2.255 1.611 1.316 16 | ATOM 5 C04 MOL 1 -2.940 1.672 2.532 17 | ATOM 6 C05 MOL 1 -2.370 1.118 3.677 18 | ATOM 7 C06 MOL 1 -1.120 0.507 3.603 19 | ATOM 8 C07 MOL 1 -0.458 0.399 2.376 20 | ATOM 9 H08 MOL 1 1.333 1.169 -1.028 21 | ATOM 10 H09 MOL 1 1.399 0.033 0.321 22 | ATOM 11 H0A MOL 1 1.394 1.815 0.618 23 | ATOM 12 H0B MOL 1 -2.699 2.044 0.423 24 | ATOM 13 H0C MOL 1 -3.915 2.149 2.581 25 | ATOM 14 H0D MOL 1 -2.901 1.163 4.624 26 | ATOM 15 H0E MOL 1 -0.656 0.111 4.503 27 | ATOM 16 H0F MOL 1 0.473 -0.156 2.334 28 | TER 29 | CONECT 1 2 30 | CONECT 2 3 31 | CONECT 3 4 32 | CONECT 4 5 33 | CONECT 5 6 34 | CONECT 6 7 35 | CONECT 3 8 36 | CONECT 1 9 37 | CONECT 1 10 38 | CONECT 1 11 39 | CONECT 4 12 40 | CONECT 5 13 41 | CONECT 6 14 42 | CONECT 7 15 43 | CONECT 8 16 44 | CONECT 7 8 45 | END 46 | -------------------------------------------------------------------------------- /Solvents/styrene/styrene.pdb: -------------------------------------------------------------------------------- 1 | TITLE styrene 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.339 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.173 1.000 1.211 15 | ATOM 4 C03 MOL 1 -0.775 1.630 2.397 16 | ATOM 5 C04 MOL 1 -1.599 1.608 3.526 17 | ATOM 6 C05 MOL 1 -2.829 0.955 3.478 18 | ATOM 7 C06 MOL 1 -3.232 0.326 2.303 19 | ATOM 8 C07 MOL 1 -2.436 0.394 1.162 20 | ATOM 9 H08 MOL 1 1.548 0.999 -0.938 21 | ATOM 10 H09 MOL 1 1.585 1.000 0.913 22 | ATOM 11 H0A MOL 1 -0.868 0.999 -0.950 23 | ATOM 12 H0B MOL 1 0.179 2.147 2.457 24 | ATOM 13 H0C MOL 1 -1.279 2.102 4.439 25 | ATOM 14 H0D MOL 1 -3.470 0.939 4.356 26 | ATOM 15 H0E MOL 1 -4.171 -0.222 2.275 27 | ATOM 16 H0F MOL 1 -2.806 -0.030 0.231 28 | TER 29 | CONECT 1 2 30 | CONECT 2 3 31 | CONECT 3 4 32 | CONECT 4 5 33 | CONECT 5 6 34 | CONECT 6 7 35 | CONECT 3 8 36 | CONECT 1 9 37 | CONECT 1 10 38 | CONECT 2 11 39 | CONECT 4 12 40 | CONECT 5 13 41 | CONECT 6 14 42 | CONECT 7 15 43 | CONECT 8 16 44 | CONECT 7 8 45 | END 46 | -------------------------------------------------------------------------------- /sample/test_charge_gen_scheme/ChargeRandomGen.txt: -------------------------------------------------------------------------------- 1 | # GAML charge scheme 2 | 3 | # symmetry_list: < [[1,9],[2,10],[3,7],[4,8],[13,14],[16,17,19,20],[22,23,24],[15,18],5,6,11,12,21] > 4 | # offset_list: < [1,11] > 5 | # counter_list: < > 6 | # total_charge: < 0.8 > 7 | # bool_neutral: < False > 8 | # bool_nozero: < True > 9 | 10 | # charge_range file: < BPYR_ChargeGenRange_BF4_ESP.txt > 11 | # For each entry, the charge_range: 12 | #ATOM 1 0.135 0.165 13 | #ATOM 2 0.278 0.318 14 | #ATOM 3 -0.28 -0.26 15 | #ATOM 4 0.266 0.306 16 | #ATOM 5 -0.111 -0.091 17 | #ATOM 6 0.27 0.31 18 | #ATOM 7 -0.286 -0.24600000000000002 19 | #ATOM 8 0.264 0.304 20 | #ATOM 9 0.119 0.149 21 | #ATOM 10 0.27 0.31 22 | #ATOM 11 -0.602 -0.552 23 | #ATOM 12 -0.224 -0.174 24 | #ATOM 13 0.219 0.259 25 | #ATOM 14 0.215 0.255 26 | #ATOM 15 -0.364 -0.334 27 | #ATOM 16 0.167 0.207 28 | #ATOM 17 0.163 0.203 29 | #ATOM 18 -0.35 -0.31 30 | #ATOM 19 0.142 0.182 31 | #ATOM 20 0.143 0.183 32 | #ATOM 21 -0.516 -0.496 33 | #ATOM 22 0.158 0.188 34 | #ATOM 23 0.151 0.181 35 | #ATOM 24 0.156 0.186 36 | 37 | 38 | # generated charge pairs: 39 | 40 | PAIR 0.123 0.314 -0.25 0.274 0.256 -0.134 -0.016 0.268 -0.106 0.285 -0.598 -0.215 0.048 41 | PAIR 0.164 0.287 -0.277 0.282 0.235 -0.14 -0.013 0.28 -0.103 0.302 -0.597 -0.184 0.039 42 | PAIR 0.099 0.312 -0.264 0.3 0.243 -0.134 -0.26 0.268 -0.098 0.299 -0.574 -0.207 0.78 43 | PAIR 0.17 0.294 -0.278 0.277 0.24 -0.138 0.001 0.276 -0.096 0.276 -0.586 -0.2 -0.003 44 | PAIR 0.145 0.3 -0.251 0.27 0.221 -0.15 -0.248 0.3 -0.096 0.297 -0.577 -0.194 0.744 45 | 46 | 47 | -------------------------------------------------------------------------------- /Solvents/N-ethylethanamine/N-ethylethanamine.pdb: -------------------------------------------------------------------------------- 1 | TITLE N-ethylethanamine 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.521 1.000 0.000 14 | ATOM 3 N02 MOL 1 -1.015 1.000 1.375 15 | ATOM 4 C03 MOL 1 -2.477 1.002 1.410 16 | ATOM 5 C04 MOL 1 -2.958 1.003 2.853 17 | ATOM 6 H05 MOL 1 1.376 0.999 -1.028 18 | ATOM 7 H06 MOL 1 1.396 0.112 0.505 19 | ATOM 8 H07 MOL 1 1.397 1.889 0.502 20 | ATOM 9 H08 MOL 1 -0.875 0.109 -0.530 21 | ATOM 10 H09 MOL 1 -0.879 1.886 -0.538 22 | ATOM 11 H0A MOL 1 -0.659 1.819 1.868 23 | ATOM 12 H0B MOL 1 -2.868 0.111 0.906 24 | ATOM 13 H0C MOL 1 -2.873 1.887 0.899 25 | ATOM 14 H0D MOL 1 -2.597 0.120 3.391 26 | ATOM 15 H0E MOL 1 -4.052 0.994 2.884 27 | ATOM 16 H0F MOL 1 -2.611 1.896 3.385 28 | TER 29 | CONECT 1 2 30 | CONECT 2 3 31 | CONECT 3 4 32 | CONECT 4 5 33 | CONECT 1 6 34 | CONECT 1 7 35 | CONECT 1 8 36 | CONECT 2 9 37 | CONECT 2 10 38 | CONECT 3 11 39 | CONECT 4 12 40 | CONECT 4 13 41 | CONECT 5 14 42 | CONECT 5 15 43 | CONECT 5 16 44 | END 45 | -------------------------------------------------------------------------------- /Solvents/2-methylphenol/2-methylphenol.pdb: -------------------------------------------------------------------------------- 1 | TITLE 2-methylphenol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.501 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.210 1.000 1.209 15 | ATOM 4 C03 MOL 1 -2.607 0.998 1.210 16 | ATOM 5 C04 MOL 1 -3.305 0.997 0.004 17 | ATOM 6 C05 MOL 1 -2.609 0.997 -1.204 18 | ATOM 7 C06 MOL 1 -1.219 0.998 -1.200 19 | ATOM 8 O07 MOL 1 -0.524 0.997 -2.378 20 | ATOM 9 H08 MOL 1 1.400 1.046 1.018 21 | ATOM 10 H09 MOL 1 1.380 1.871 -0.544 22 | ATOM 11 H0A MOL 1 1.377 0.085 -0.468 23 | ATOM 12 H0B MOL 1 -0.678 1.000 2.157 24 | ATOM 13 H0C MOL 1 -3.146 0.997 2.154 25 | ATOM 14 H0D MOL 1 -4.392 0.995 0.008 26 | ATOM 15 H0E MOL 1 -3.167 0.995 -2.135 27 | ATOM 16 H0F MOL 1 -1.159 0.995 -3.111 28 | TER 29 | CONECT 1 2 30 | CONECT 2 3 31 | CONECT 3 4 32 | CONECT 4 5 33 | CONECT 5 6 34 | CONECT 2 7 35 | CONECT 7 8 36 | CONECT 1 9 37 | CONECT 1 10 38 | CONECT 1 11 39 | CONECT 3 12 40 | CONECT 4 13 41 | CONECT 5 14 42 | CONECT 6 15 43 | CONECT 8 16 44 | CONECT 6 7 45 | END 46 | -------------------------------------------------------------------------------- /Solvents/4-methylphenol/4-methylphenol.pdb: -------------------------------------------------------------------------------- 1 | TITLE 4-methylphenol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.500 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.219 1.000 1.203 15 | ATOM 4 C03 MOL 1 -2.617 0.998 1.191 16 | ATOM 5 C04 MOL 1 -3.290 0.997 -0.026 17 | ATOM 6 O05 MOL 1 -4.652 0.994 -0.083 18 | ATOM 7 C06 MOL 1 -2.589 0.997 -1.225 19 | ATOM 8 C07 MOL 1 -1.197 0.998 -1.216 20 | ATOM 9 H08 MOL 1 1.401 1.091 1.015 21 | ATOM 10 H09 MOL 1 1.378 1.844 -0.586 22 | ATOM 11 H0A MOL 1 1.375 0.065 -0.429 23 | ATOM 12 H0B MOL 1 -0.695 1.000 2.155 24 | ATOM 13 H0C MOL 1 -3.154 0.997 2.134 25 | ATOM 14 H0D MOL 1 -4.996 0.952 0.824 26 | ATOM 15 H0E MOL 1 -3.127 0.995 -2.169 27 | ATOM 16 H0F MOL 1 -0.655 0.997 -2.158 28 | TER 29 | CONECT 1 2 30 | CONECT 2 3 31 | CONECT 3 4 32 | CONECT 4 5 33 | CONECT 5 6 34 | CONECT 5 7 35 | CONECT 2 8 36 | CONECT 1 9 37 | CONECT 1 10 38 | CONECT 1 11 39 | CONECT 3 12 40 | CONECT 4 13 41 | CONECT 6 14 42 | CONECT 7 15 43 | CONECT 8 16 44 | CONECT 7 8 45 | END 46 | -------------------------------------------------------------------------------- /Solvents/benzylalcohol/benzylalcohol.pdb: -------------------------------------------------------------------------------- 1 | TITLE benzylalcohol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 O00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.419 1.000 0.000 14 | ATOM 3 C02 MOL 1 -0.902 1.000 1.422 15 | ATOM 4 C03 MOL 1 -1.147 2.208 2.090 16 | ATOM 5 C04 MOL 1 -1.594 2.208 3.413 17 | ATOM 6 C05 MOL 1 -1.800 1.002 4.079 18 | ATOM 7 C06 MOL 1 -1.559 -0.205 3.424 19 | ATOM 8 C07 MOL 1 -1.061 -0.207 2.118 20 | ATOM 9 H08 MOL 1 1.281 1.001 -0.929 21 | ATOM 10 H09 MOL 1 -0.778 0.112 -0.532 22 | ATOM 11 H0A MOL 1 -0.778 1.886 -0.535 23 | ATOM 12 H0B MOL 1 -0.988 3.155 1.580 24 | ATOM 13 H0C MOL 1 -1.779 3.150 3.921 25 | ATOM 14 H0D MOL 1 -2.147 1.003 5.109 26 | ATOM 15 H0E MOL 1 -1.759 -1.146 3.930 27 | ATOM 16 H0F MOL 1 -0.795 -1.148 1.643 28 | TER 29 | CONECT 1 2 30 | CONECT 2 3 31 | CONECT 3 4 32 | CONECT 4 5 33 | CONECT 5 6 34 | CONECT 6 7 35 | CONECT 3 8 36 | CONECT 1 9 37 | CONECT 2 10 38 | CONECT 2 11 39 | CONECT 4 12 40 | CONECT 5 13 41 | CONECT 6 14 42 | CONECT 7 15 43 | CONECT 8 16 44 | CONECT 7 8 45 | END 46 | -------------------------------------------------------------------------------- /Solvents/ethylpropionate/ethylpropionate.pdb: -------------------------------------------------------------------------------- 1 | TITLE ethylpropionate 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.518 1.000 0.000 14 | ATOM 3 O02 MOL 1 -0.960 1.000 1.364 15 | ATOM 4 C03 MOL 1 -1.075 -0.231 1.934 16 | ATOM 5 O04 MOL 1 -1.058 -1.296 1.336 17 | ATOM 6 C05 MOL 1 -1.136 -0.074 3.435 18 | ATOM 7 C06 MOL 1 -1.138 -1.416 4.144 19 | ATOM 8 H07 MOL 1 1.395 1.001 -1.019 20 | ATOM 9 H08 MOL 1 1.389 0.124 0.531 21 | ATOM 10 H09 MOL 1 1.377 1.882 0.529 22 | ATOM 11 H0A MOL 1 -0.920 0.151 -0.564 23 | ATOM 12 H0B MOL 1 -0.894 1.915 -0.470 24 | ATOM 13 H0C MOL 1 -2.032 0.495 3.701 25 | ATOM 14 H0D MOL 1 -0.246 0.487 3.744 26 | ATOM 15 H0E MOL 1 -2.046 -1.982 3.911 27 | ATOM 16 H0F MOL 1 -1.088 -1.273 5.227 28 | ATOM 17 H0G MOL 1 -0.279 -2.024 3.838 29 | TER 30 | CONECT 1 2 31 | CONECT 2 3 32 | CONECT 3 4 33 | CONECT 4 5 34 | CONECT 4 6 35 | CONECT 6 7 36 | CONECT 1 8 37 | CONECT 1 9 38 | CONECT 1 10 39 | CONECT 2 11 40 | CONECT 2 12 41 | CONECT 6 13 42 | CONECT 6 14 43 | CONECT 7 15 44 | CONECT 7 16 45 | CONECT 7 17 46 | END 47 | -------------------------------------------------------------------------------- /Solvents/acetophenone/acetophenone.pdb: -------------------------------------------------------------------------------- 1 | TITLE acetophenone 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.506 1.000 0.000 14 | ATOM 3 O02 MOL 1 -1.140 1.000 1.054 15 | ATOM 4 C03 MOL 1 -1.228 0.998 -1.308 16 | ATOM 5 C04 MOL 1 -0.552 0.997 -2.534 17 | ATOM 6 C05 MOL 1 -1.273 0.997 -3.732 18 | ATOM 7 C06 MOL 1 -2.667 0.998 -3.710 19 | ATOM 8 C07 MOL 1 -3.344 1.000 -2.492 20 | ATOM 9 C08 MOL 1 -2.630 0.997 -1.295 21 | ATOM 10 H09 MOL 1 1.358 1.046 1.033 22 | ATOM 11 H0A MOL 1 1.380 1.879 -0.527 23 | ATOM 12 H0B MOL 1 1.377 0.078 -0.450 24 | ATOM 13 H0C MOL 1 0.533 0.994 -2.586 25 | ATOM 14 H0D MOL 1 -0.745 0.997 -4.683 26 | ATOM 15 H0E MOL 1 -3.225 0.997 -4.643 27 | ATOM 16 H0F MOL 1 -4.431 1.005 -2.473 28 | ATOM 17 H0G MOL 1 -3.169 0.994 -0.349 29 | TER 30 | CONECT 1 2 31 | CONECT 2 3 32 | CONECT 2 4 33 | CONECT 4 5 34 | CONECT 5 6 35 | CONECT 6 7 36 | CONECT 7 8 37 | CONECT 4 9 38 | CONECT 1 10 39 | CONECT 1 11 40 | CONECT 1 12 41 | CONECT 5 13 42 | CONECT 6 14 43 | CONECT 7 15 44 | CONECT 8 16 45 | CONECT 9 17 46 | CONECT 8 9 47 | END 48 | -------------------------------------------------------------------------------- /Solvents/cyclohexanone/cyclohexanone.pdb: -------------------------------------------------------------------------------- 1 | TITLE cyclohexanone 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 O00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.230 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.025 1.000 1.285 15 | ATOM 4 C03 MOL 1 -2.133 2.042 1.211 16 | ATOM 5 C04 MOL 1 -2.994 1.860 -0.038 17 | ATOM 6 C05 MOL 1 -2.142 1.907 -1.305 18 | ATOM 7 C06 MOL 1 -1.027 0.870 -1.278 19 | ATOM 8 H07 MOL 1 -0.357 1.219 2.124 20 | ATOM 9 H08 MOL 1 -1.439 -0.004 1.428 21 | ATOM 10 H09 MOL 1 -1.689 3.046 1.197 22 | ATOM 11 H0A MOL 1 -2.760 1.977 2.107 23 | ATOM 12 H0B MOL 1 -3.754 2.649 -0.077 24 | ATOM 13 H0C MOL 1 -3.524 0.901 0.017 25 | ATOM 14 H0D MOL 1 -1.705 2.908 -1.404 26 | ATOM 15 H0E MOL 1 -2.776 1.742 -2.183 27 | ATOM 16 H0F MOL 1 -0.360 1.010 -2.135 28 | ATOM 17 H0G MOL 1 -1.433 -0.146 -1.321 29 | TER 30 | CONECT 1 2 31 | CONECT 2 3 32 | CONECT 3 4 33 | CONECT 4 5 34 | CONECT 5 6 35 | CONECT 2 7 36 | CONECT 3 8 37 | CONECT 3 9 38 | CONECT 4 10 39 | CONECT 4 11 40 | CONECT 5 12 41 | CONECT 5 13 42 | CONECT 6 14 43 | CONECT 6 15 44 | CONECT 7 16 45 | CONECT 7 17 46 | CONECT 6 7 47 | END 48 | -------------------------------------------------------------------------------- /Solvents/quinoline/quinoline.pdb: -------------------------------------------------------------------------------- 1 | TITLE quinoline 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.390 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.086 1.000 1.213 15 | ATOM 4 C03 MOL 1 -0.423 1.000 2.434 16 | ATOM 5 N04 MOL 1 -1.136 1.001 3.574 17 | ATOM 6 C05 MOL 1 -0.459 1.003 4.744 18 | ATOM 7 C06 MOL 1 0.919 1.003 4.837 19 | ATOM 8 C07 MOL 1 1.652 1.001 3.656 20 | ATOM 9 C08 MOL 1 0.989 1.000 2.423 21 | ATOM 10 C09 MOL 1 1.687 1.000 1.212 22 | ATOM 11 H0A MOL 1 1.546 1.001 -0.940 23 | ATOM 12 H0B MOL 1 -0.937 1.001 -0.939 24 | ATOM 13 H0C MOL 1 -2.173 1.001 1.207 25 | ATOM 14 H0D MOL 1 -1.082 1.005 5.634 26 | ATOM 15 H0E MOL 1 1.409 1.005 5.804 27 | ATOM 16 H0F MOL 1 2.737 1.003 3.701 28 | ATOM 17 H0G MOL 1 2.775 1.001 1.203 29 | TER 30 | CONECT 1 2 31 | CONECT 2 3 32 | CONECT 3 4 33 | CONECT 4 5 34 | CONECT 5 6 35 | CONECT 6 7 36 | CONECT 7 8 37 | CONECT 4 9 38 | CONECT 1 10 39 | CONECT 1 11 40 | CONECT 2 12 41 | CONECT 3 13 42 | CONECT 6 14 43 | CONECT 7 15 44 | CONECT 8 16 45 | CONECT 10 17 46 | CONECT 8 9 47 | CONECT 9 10 48 | END 49 | -------------------------------------------------------------------------------- /Solvents/1-pentanol/1-pentanol.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1-pentanol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.520 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.079 1.000 1.423 15 | ATOM 4 C03 MOL 1 -2.606 1.002 1.420 16 | ATOM 5 C04 MOL 1 -3.168 1.000 2.835 17 | ATOM 6 O05 MOL 1 -4.589 1.000 2.788 18 | ATOM 7 H06 MOL 1 1.378 0.999 -1.027 19 | ATOM 8 H07 MOL 1 1.391 0.112 0.507 20 | ATOM 9 H08 MOL 1 1.391 1.889 0.505 21 | ATOM 10 H09 MOL 1 -0.879 0.117 -0.541 22 | ATOM 11 H0A MOL 1 -0.879 1.883 -0.541 23 | ATOM 12 H0B MOL 1 -0.712 1.883 1.961 24 | ATOM 13 H0C MOL 1 -0.713 0.117 1.960 25 | ATOM 14 H0D MOL 1 -2.986 0.127 0.878 26 | ATOM 15 H0E MOL 1 -2.981 1.879 0.878 27 | ATOM 16 H0F MOL 1 -2.839 1.881 3.395 28 | ATOM 17 H0G MOL 1 -2.849 0.106 3.379 29 | ATOM 18 H0H MOL 1 -4.865 1.808 2.322 30 | TER 31 | CONECT 1 2 32 | CONECT 2 3 33 | CONECT 3 4 34 | CONECT 4 5 35 | CONECT 5 6 36 | CONECT 1 7 37 | CONECT 1 8 38 | CONECT 1 9 39 | CONECT 2 10 40 | CONECT 2 11 41 | CONECT 3 12 42 | CONECT 3 13 43 | CONECT 4 14 44 | CONECT 4 15 45 | CONECT 5 16 46 | CONECT 5 17 47 | CONECT 6 18 48 | END 49 | -------------------------------------------------------------------------------- /Solvents/2-methyl-2-butanol/2-methyl-2-butanol.pdb: -------------------------------------------------------------------------------- 1 | TITLE 2-methyl-2-butanol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.522 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.186 1.000 1.390 15 | ATOM 4 C03 MOL 1 -0.818 -0.235 2.214 16 | ATOM 5 C04 MOL 1 -0.873 2.274 2.176 17 | ATOM 6 O05 MOL 1 -2.605 0.980 1.186 18 | ATOM 7 H06 MOL 1 1.370 1.001 -1.031 19 | ATOM 8 H07 MOL 1 1.401 0.109 0.492 20 | ATOM 9 H08 MOL 1 1.403 1.887 0.497 21 | ATOM 10 H09 MOL 1 -0.872 0.128 -0.568 22 | ATOM 11 H0A MOL 1 -0.876 1.871 -0.567 23 | ATOM 12 H0B MOL 1 0.241 -0.247 2.488 24 | ATOM 13 H0C MOL 1 -1.045 -1.154 1.662 25 | ATOM 14 H0D MOL 1 -1.408 -0.275 3.138 26 | ATOM 15 H0E MOL 1 0.187 2.349 2.436 27 | ATOM 16 H0F MOL 1 -1.455 2.309 3.104 28 | ATOM 17 H0G MOL 1 -1.155 3.164 1.601 29 | ATOM 18 H0H MOL 1 -2.827 0.161 0.710 30 | TER 31 | CONECT 1 2 32 | CONECT 2 3 33 | CONECT 3 4 34 | CONECT 3 5 35 | CONECT 3 6 36 | CONECT 1 7 37 | CONECT 1 8 38 | CONECT 1 9 39 | CONECT 2 10 40 | CONECT 2 11 41 | CONECT 4 12 42 | CONECT 4 13 43 | CONECT 4 14 44 | CONECT 5 15 45 | CONECT 5 16 46 | CONECT 5 17 47 | CONECT 6 18 48 | END 49 | -------------------------------------------------------------------------------- /Solvents/methylbenzoate/methylbenzoate.pdb: -------------------------------------------------------------------------------- 1 | TITLE methylbenzoate 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 O01 MOL 1 -0.428 1.000 0.000 14 | ATOM 3 C02 MOL 1 -0.979 1.000 1.240 15 | ATOM 4 O03 MOL 1 -0.363 1.000 2.294 16 | ATOM 5 C04 MOL 1 -2.465 0.998 1.151 17 | ATOM 6 C05 MOL 1 -3.197 0.886 2.342 18 | ATOM 7 C06 MOL 1 -4.593 0.878 2.311 19 | ATOM 8 C07 MOL 1 -5.264 0.982 1.093 20 | ATOM 9 C08 MOL 1 -4.540 1.094 -0.094 21 | ATOM 10 C09 MOL 1 -3.146 1.103 -0.070 22 | ATOM 11 H0A MOL 1 1.337 0.906 -1.036 23 | ATOM 12 H0B MOL 1 1.387 0.146 0.567 24 | ATOM 13 H0C MOL 1 1.379 1.943 0.406 25 | ATOM 14 H0D MOL 1 -2.682 0.803 3.297 26 | ATOM 15 H0E MOL 1 -5.155 0.790 3.238 27 | ATOM 16 H0F MOL 1 -6.351 0.975 1.070 28 | ATOM 17 H0G MOL 1 -5.065 1.174 -1.043 29 | ATOM 18 H0H MOL 1 -2.601 1.189 -1.006 30 | TER 31 | CONECT 1 2 32 | CONECT 2 3 33 | CONECT 3 4 34 | CONECT 3 5 35 | CONECT 5 6 36 | CONECT 6 7 37 | CONECT 7 8 38 | CONECT 8 9 39 | CONECT 5 10 40 | CONECT 1 11 41 | CONECT 1 12 42 | CONECT 1 13 43 | CONECT 6 14 44 | CONECT 7 15 45 | CONECT 8 16 46 | CONECT 9 17 47 | CONECT 10 18 48 | CONECT 9 10 49 | END 50 | -------------------------------------------------------------------------------- /Solvents/2-hexanone/2-hexanone.pdb: -------------------------------------------------------------------------------- 1 | TITLE 2-hexanone 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.521 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.073 1.000 1.424 15 | ATOM 4 C03 MOL 1 -2.600 0.998 1.441 16 | ATOM 5 C04 MOL 1 -3.157 0.996 2.854 17 | ATOM 6 C05 MOL 1 -4.656 0.993 2.994 18 | ATOM 7 O06 MOL 1 -2.436 0.999 3.853 19 | ATOM 8 H07 MOL 1 1.380 1.001 -1.026 20 | ATOM 9 H08 MOL 1 1.391 0.112 0.506 21 | ATOM 10 H09 MOL 1 1.391 1.887 0.509 22 | ATOM 11 H0A MOL 1 -0.881 0.117 -0.541 23 | ATOM 12 H0B MOL 1 -0.881 1.883 -0.541 24 | ATOM 13 H0C MOL 1 -0.701 1.881 1.962 25 | ATOM 14 H0D MOL 1 -0.699 0.120 1.963 26 | ATOM 15 H0E MOL 1 -2.979 0.107 0.928 27 | ATOM 16 H0F MOL 1 -2.981 1.889 0.928 28 | ATOM 17 H0G MOL 1 -5.135 0.992 2.012 29 | ATOM 18 H0H MOL 1 -4.968 1.890 3.535 30 | ATOM 19 H0I MOL 1 -4.964 0.095 3.535 31 | TER 32 | CONECT 1 2 33 | CONECT 2 3 34 | CONECT 3 4 35 | CONECT 4 5 36 | CONECT 5 6 37 | CONECT 5 7 38 | CONECT 1 8 39 | CONECT 1 9 40 | CONECT 1 10 41 | CONECT 2 11 42 | CONECT 2 12 43 | CONECT 3 13 44 | CONECT 3 14 45 | CONECT 4 15 46 | CONECT 4 16 47 | CONECT 6 17 48 | CONECT 6 18 49 | CONECT 6 19 50 | END 51 | -------------------------------------------------------------------------------- /Solvents/chloroform/chloroform.itp: -------------------------------------------------------------------------------- 1 | ; chloroform 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_803 Cl803 35.4500 0.000 A 3.40000E-01 1.25520E+00 18 | opls_804 H804 1.0080 0.277 A 2.50000E-01 1.25520E-01 19 | opls_800 Cl800 35.4500 -0.008 A 3.40000E-01 1.25520E+00 20 | opls_801 C801 12.0110 -0.253 A 3.50000E-01 2.76144E-01 21 | opls_802 Cl802 35.4500 0.000 A 3.40000E-01 1.25520E+00 22 | 23 | 24 | [ moleculetype ] 25 | ; name nrexcl 26 | MOL 3 27 | 28 | 29 | [ atoms ] 30 | ; nr type resnr residue atom cgnr charge mass 31 | 1 opls_800 1 MOL Cl0 1 -0.008 35.4500 32 | 2 opls_801 1 MOL C01 1 -0.253 12.0110 33 | 3 opls_800 1 MOL Cl1 1 -0.008 35.4500 34 | 4 opls_800 1 MOL Cl2 1 -0.008 35.4500 35 | 5 opls_804 1 MOL H04 1 0.277 1.0080 36 | 37 | 38 | [ bonds ] 39 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 40 | 2 1 1 0.1781 205016.000 41 | 3 2 1 0.1781 205016.000 42 | 4 2 1 0.1781 205016.000 43 | 5 2 1 0.1090 284512.000 44 | 45 | 46 | [ angles ] 47 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 48 | 1 2 3 1 111.700 652.704 49 | 1 2 4 1 111.700 652.704 50 | 1 2 5 1 107.600 426.768 51 | 3 2 4 1 111.700 652.704 52 | 3 2 5 1 107.600 426.768 53 | 4 2 5 1 107.600 426.768 54 | 55 | 56 | -------------------------------------------------------------------------------- /Solvents/dibromomethane/dibromomethane.itp: -------------------------------------------------------------------------------- 1 | ; dibromomethane 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_803 H803 1.0080 0.033 A 2.50000E-01 1.25520E-01 18 | opls_800 Br800 79.9040 -0.188 A 3.47000E-01 1.96648E+00 19 | opls_802 Br802 79.9040 0.000 A 3.47000E-01 1.96648E+00 20 | opls_801 C801 12.0110 0.31 A 3.50000E-01 2.76144E-01 21 | opls_804 H804 1.0080 0.000 A 2.50000E-01 1.25520E-01 22 | 23 | 24 | [ moleculetype ] 25 | ; name nrexcl 26 | MOL 3 27 | 28 | 29 | [ atoms ] 30 | ; nr type resnr residue atom cgnr charge mass 31 | 1 opls_800 1 MOL Br0 1 -0.188 79.9040 32 | 2 opls_801 1 MOL C01 1 0.31 12.0110 33 | 3 opls_800 1 MOL Br2 1 -0.188 79.9040 34 | 4 opls_803 1 MOL H03 1 0.033 1.0080 35 | 5 opls_803 1 MOL H04 1 0.033 1.0080 36 | 37 | 38 | [ bonds ] 39 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 40 | 2 1 1 0.1945 205016.000 41 | 3 2 1 0.1945 205016.000 42 | 4 2 1 0.1090 284512.000 43 | 5 2 1 0.1090 284512.000 44 | 45 | 46 | [ angles ] 47 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 48 | 1 2 3 1 111.700 652.704 49 | 1 2 4 1 107.600 426.768 50 | 1 2 5 1 107.600 426.768 51 | 3 2 4 1 107.600 426.768 52 | 3 2 5 1 107.600 426.768 53 | 4 2 5 1 107.800 276.144 54 | 55 | 56 | -------------------------------------------------------------------------------- /Solvents/dichloromethane/dichloromethane.itp: -------------------------------------------------------------------------------- 1 | ; dichloromethane 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_803 H803 1.0080 0.237 A 2.50000E-01 1.25520E-01 18 | opls_804 H804 1.0080 0.000 A 2.50000E-01 1.25520E-01 19 | opls_800 Cl800 35.4500 -0.046 A 3.40000E-01 1.25520E+00 20 | opls_801 C801 12.0110 -0.382 A 3.50000E-01 2.76144E-01 21 | opls_802 Cl802 35.4500 0.000 A 3.40000E-01 1.25520E+00 22 | 23 | 24 | [ moleculetype ] 25 | ; name nrexcl 26 | MOL 3 27 | 28 | 29 | [ atoms ] 30 | ; nr type resnr residue atom cgnr charge mass 31 | 1 opls_800 1 MOL Cl0 1 -0.046 35.4500 32 | 2 opls_801 1 MOL C01 1 -0.382 12.0110 33 | 3 opls_800 1 MOL Cl1 1 -0.046 35.4500 34 | 4 opls_803 1 MOL H03 1 0.237 1.0080 35 | 5 opls_803 1 MOL H04 1 0.237 1.0080 36 | 37 | 38 | [ bonds ] 39 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 40 | 2 1 1 0.1781 205016.000 41 | 3 2 1 0.1781 205016.000 42 | 4 2 1 0.1090 284512.000 43 | 5 2 1 0.1090 284512.000 44 | 45 | 46 | [ angles ] 47 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 48 | 1 2 3 1 111.700 652.704 49 | 1 2 4 1 107.600 426.768 50 | 1 2 5 1 107.600 426.768 51 | 3 2 4 1 107.600 426.768 52 | 3 2 5 1 107.600 426.768 53 | 4 2 5 1 107.800 276.144 54 | 55 | 56 | -------------------------------------------------------------------------------- /Solvents/cyclohexanamine/cyclohexanamine.pdb: -------------------------------------------------------------------------------- 1 | TITLE cyclohexanamine 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 N00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.465 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.021 1.000 1.431 15 | ATOM 4 C03 MOL 1 -0.810 2.330 2.155 16 | ATOM 5 C04 MOL 1 -1.358 3.502 1.346 17 | ATOM 6 C05 MOL 1 -0.798 3.530 -0.074 18 | ATOM 7 C06 MOL 1 -1.001 2.202 -0.790 19 | ATOM 8 H07 MOL 1 1.341 0.225 0.568 20 | ATOM 9 H08 MOL 1 1.355 1.847 0.441 21 | ATOM 10 H09 MOL 1 -0.788 0.080 -0.501 22 | ATOM 11 H0A MOL 1 -0.572 0.188 2.016 23 | ATOM 12 H0B MOL 1 -2.098 0.790 1.387 24 | ATOM 13 H0C MOL 1 0.258 2.484 2.351 25 | ATOM 14 H0D MOL 1 -1.307 2.296 3.132 26 | ATOM 15 H0E MOL 1 -1.120 4.443 1.855 27 | ATOM 16 H0F MOL 1 -2.452 3.429 1.301 28 | ATOM 17 H0G MOL 1 0.270 3.777 -0.041 29 | ATOM 18 H0H MOL 1 -1.288 4.328 -0.643 30 | ATOM 19 H0I MOL 1 -0.535 2.246 -1.782 31 | ATOM 20 H0J MOL 1 -2.076 2.057 -0.960 32 | TER 33 | CONECT 1 2 34 | CONECT 2 3 35 | CONECT 3 4 36 | CONECT 4 5 37 | CONECT 5 6 38 | CONECT 2 7 39 | CONECT 1 8 40 | CONECT 1 9 41 | CONECT 2 10 42 | CONECT 3 11 43 | CONECT 3 12 44 | CONECT 4 13 45 | CONECT 4 14 46 | CONECT 5 15 47 | CONECT 5 16 48 | CONECT 6 17 49 | CONECT 6 18 50 | CONECT 7 19 51 | CONECT 7 20 52 | CONECT 6 7 53 | END 54 | -------------------------------------------------------------------------------- /Solvents/diisopropylether/diisopropylether.pdb: -------------------------------------------------------------------------------- 1 | TITLE diisopropylether 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.527 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.048 1.000 1.434 15 | ATOM 4 O03 MOL 1 -1.071 2.160 -0.633 16 | ATOM 5 C04 MOL 1 -0.765 2.347 -2.018 17 | ATOM 6 C05 MOL 1 -1.309 1.220 -2.885 18 | ATOM 7 C06 MOL 1 -1.390 3.679 -2.427 19 | ATOM 8 H07 MOL 1 1.393 0.171 0.594 20 | ATOM 9 H08 MOL 1 1.392 1.941 0.399 21 | ATOM 10 H09 MOL 1 1.393 0.889 -1.015 22 | ATOM 11 H0A MOL 1 -0.898 0.095 -0.493 23 | ATOM 12 H0B MOL 1 -0.865 1.965 1.920 24 | ATOM 13 H0C MOL 1 -0.585 0.209 2.032 25 | ATOM 14 H0D MOL 1 -2.133 0.847 1.442 26 | ATOM 15 H0E MOL 1 0.319 2.436 -2.149 27 | ATOM 16 H0F MOL 1 -2.346 0.986 -2.620 28 | ATOM 17 H0G MOL 1 -0.726 0.305 -2.741 29 | ATOM 18 H0H MOL 1 -1.262 1.476 -3.948 30 | ATOM 19 H0I MOL 1 -2.476 3.665 -2.281 31 | ATOM 20 H0J MOL 1 -1.179 3.911 -3.476 32 | ATOM 21 H0K MOL 1 -0.998 4.492 -1.805 33 | TER 34 | CONECT 1 2 35 | CONECT 2 3 36 | CONECT 2 4 37 | CONECT 4 5 38 | CONECT 5 6 39 | CONECT 5 7 40 | CONECT 1 8 41 | CONECT 1 9 42 | CONECT 1 10 43 | CONECT 2 11 44 | CONECT 3 12 45 | CONECT 3 13 46 | CONECT 3 14 47 | CONECT 5 15 48 | CONECT 6 16 49 | CONECT 6 17 50 | CONECT 6 18 51 | CONECT 7 19 52 | CONECT 7 20 53 | CONECT 7 21 54 | END 55 | -------------------------------------------------------------------------------- /Solvents/2-heptanone/2-heptanone.pdb: -------------------------------------------------------------------------------- 1 | TITLE 2-heptanone 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.520 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.089 1.000 1.420 15 | ATOM 4 C03 MOL 1 -2.619 0.998 1.394 16 | ATOM 5 C04 MOL 1 -3.214 0.996 2.800 17 | ATOM 6 C05 MOL 1 -4.734 0.996 2.775 18 | ATOM 7 C06 MOL 1 -5.435 0.993 4.108 19 | ATOM 8 O07 MOL 1 -5.382 0.998 1.729 20 | ATOM 9 H08 MOL 1 1.378 0.999 -1.027 21 | ATOM 10 H09 MOL 1 1.392 0.112 0.507 22 | ATOM 11 H0A MOL 1 1.392 1.888 0.505 23 | ATOM 12 H0B MOL 1 -0.877 0.118 -0.543 24 | ATOM 13 H0C MOL 1 -0.876 1.883 -0.542 25 | ATOM 14 H0D MOL 1 -0.730 1.884 1.960 26 | ATOM 15 H0E MOL 1 -0.728 0.117 1.961 27 | ATOM 16 H0F MOL 1 -2.974 0.117 0.844 28 | ATOM 17 H0G MOL 1 -2.976 1.879 0.846 29 | ATOM 18 H0H MOL 1 -2.885 1.887 3.347 30 | ATOM 19 H0I MOL 1 -2.884 0.105 3.345 31 | ATOM 20 H0J MOL 1 -4.709 0.991 4.925 32 | ATOM 21 H0K MOL 1 -6.054 0.095 4.186 33 | ATOM 22 H0M MOL 1 -6.054 1.890 4.191 34 | TER 35 | CONECT 1 2 36 | CONECT 2 3 37 | CONECT 3 4 38 | CONECT 4 5 39 | CONECT 5 6 40 | CONECT 6 7 41 | CONECT 6 8 42 | CONECT 1 9 43 | CONECT 1 10 44 | CONECT 1 11 45 | CONECT 2 12 46 | CONECT 2 13 47 | CONECT 3 14 48 | CONECT 3 15 49 | CONECT 4 16 50 | CONECT 4 17 51 | CONECT 5 18 52 | CONECT 5 19 53 | CONECT 7 20 54 | CONECT 7 21 55 | CONECT 7 22 56 | END 57 | -------------------------------------------------------------------------------- /Solvents/triethylamine/triethylamine.pdb: -------------------------------------------------------------------------------- 1 | TITLE triethylamine 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.526 1.000 0.000 14 | ATOM 3 N02 MOL 1 -1.144 1.000 1.339 15 | ATOM 4 C03 MOL 1 -0.681 2.089 2.212 16 | ATOM 5 C04 MOL 1 -1.087 3.501 1.800 17 | ATOM 6 C05 MOL 1 -2.609 0.919 1.200 18 | ATOM 7 C06 MOL 1 -3.363 0.771 2.517 19 | ATOM 8 H07 MOL 1 1.371 0.794 -1.010 20 | ATOM 9 H08 MOL 1 1.399 0.229 0.666 21 | ATOM 10 H09 MOL 1 1.402 1.973 0.300 22 | ATOM 11 H0A MOL 1 -0.840 0.087 -0.523 23 | ATOM 12 H0B MOL 1 -0.881 1.846 -0.601 24 | ATOM 13 H0C MOL 1 0.410 2.048 2.306 25 | ATOM 14 H0D MOL 1 -1.034 1.907 3.234 26 | ATOM 15 H0E MOL 1 -0.818 3.720 0.763 27 | ATOM 16 H0F MOL 1 -0.572 4.231 2.435 28 | ATOM 17 H0G MOL 1 -2.163 3.659 1.921 29 | ATOM 18 H0H MOL 1 -2.853 0.034 0.598 30 | ATOM 19 H0I MOL 1 -3.002 1.788 0.656 31 | ATOM 20 H0J MOL 1 -2.976 -0.068 3.103 32 | ATOM 21 H0K MOL 1 -4.423 0.580 2.317 33 | ATOM 22 H0M MOL 1 -3.305 1.680 3.126 34 | TER 35 | CONECT 1 2 36 | CONECT 2 3 37 | CONECT 3 4 38 | CONECT 4 5 39 | CONECT 3 6 40 | CONECT 6 7 41 | CONECT 1 8 42 | CONECT 1 9 43 | CONECT 1 10 44 | CONECT 2 11 45 | CONECT 2 12 46 | CONECT 4 13 47 | CONECT 4 14 48 | CONECT 5 15 49 | CONECT 5 16 50 | CONECT 5 17 51 | CONECT 6 18 52 | CONECT 6 19 53 | CONECT 7 20 54 | CONECT 7 21 55 | CONECT 7 22 56 | END 57 | -------------------------------------------------------------------------------- /Solvents/2,4-dimethyl-3-pentanone/2,4-dimethyl-3-pentanone.pdb: -------------------------------------------------------------------------------- 1 | TITLE 2,4-dimethyl-3-pentanone 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.531 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.053 1.000 1.433 15 | ATOM 4 C03 MOL 1 -1.053 2.227 -0.747 16 | ATOM 5 O04 MOL 1 -0.477 3.314 -0.655 17 | ATOM 6 C05 MOL 1 -2.309 2.057 -1.612 18 | ATOM 7 C06 MOL 1 -3.516 1.677 -0.762 19 | ATOM 8 C07 MOL 1 -2.605 3.341 -2.390 20 | ATOM 9 H08 MOL 1 1.389 0.110 0.505 21 | ATOM 10 H09 MOL 1 1.402 1.880 0.516 22 | ATOM 11 H0A MOL 1 1.389 1.007 -1.023 23 | ATOM 12 H0B MOL 1 -0.864 0.096 -0.521 24 | ATOM 13 H0C MOL 1 -0.953 1.988 1.896 25 | ATOM 14 H0D MOL 1 -0.516 0.275 2.053 26 | ATOM 15 H0E MOL 1 -2.114 0.733 1.464 27 | ATOM 16 H0F MOL 1 -2.103 1.262 -2.337 28 | ATOM 17 H0G MOL 1 -3.595 2.313 0.126 29 | ATOM 18 H0H MOL 1 -3.438 0.638 -0.426 30 | ATOM 19 H0I MOL 1 -4.447 1.766 -1.331 31 | ATOM 20 H0J MOL 1 -2.788 4.184 -1.713 32 | ATOM 21 H0K MOL 1 -3.490 3.218 -3.023 33 | ATOM 22 H0M MOL 1 -1.762 3.610 -3.034 34 | TER 35 | CONECT 1 2 36 | CONECT 2 3 37 | CONECT 2 4 38 | CONECT 4 5 39 | CONECT 4 6 40 | CONECT 6 7 41 | CONECT 6 8 42 | CONECT 1 9 43 | CONECT 1 10 44 | CONECT 1 11 45 | CONECT 2 12 46 | CONECT 3 13 47 | CONECT 3 14 48 | CONECT 3 15 49 | CONECT 6 16 50 | CONECT 7 17 51 | CONECT 7 18 52 | CONECT 7 19 53 | CONECT 8 20 54 | CONECT 8 21 55 | CONECT 8 22 56 | END 57 | -------------------------------------------------------------------------------- /Solvents/N-1-methylethyl--2-propanamine/N-1-methylethyl--2-propanamine.pdb: -------------------------------------------------------------------------------- 1 | TITLE N-1-methylethyl--2-propanamine 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.530 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.045 1.000 1.443 15 | ATOM 4 N03 MOL 1 -1.104 2.168 -0.678 16 | ATOM 5 C04 MOL 1 -0.786 2.306 -2.104 17 | ATOM 6 C05 MOL 1 -1.294 1.130 -2.938 18 | ATOM 7 C06 MOL 1 -1.424 3.607 -2.605 19 | ATOM 8 H07 MOL 1 1.384 0.160 0.591 20 | ATOM 9 H08 MOL 1 1.401 1.924 0.431 21 | ATOM 10 H09 MOL 1 1.402 0.887 -1.012 22 | ATOM 11 H0A MOL 1 -0.886 0.076 -0.467 23 | ATOM 12 H0B MOL 1 -0.806 1.938 1.957 24 | ATOM 13 H0C MOL 1 -0.595 0.181 2.017 25 | ATOM 14 H0D MOL 1 -2.132 0.866 1.467 26 | ATOM 15 H0E MOL 1 -0.819 3.016 -0.187 27 | ATOM 16 H0F MOL 1 0.297 2.406 -2.243 28 | ATOM 17 H0G MOL 1 -2.351 0.926 -2.739 29 | ATOM 18 H0H MOL 1 -0.723 0.220 -2.730 30 | ATOM 19 H0I MOL 1 -1.191 1.340 -4.008 31 | ATOM 20 H0J MOL 1 -2.515 3.586 -2.505 32 | ATOM 21 H0K MOL 1 -1.186 3.772 -3.662 33 | ATOM 22 H0M MOL 1 -1.047 4.471 -2.046 34 | TER 35 | CONECT 1 2 36 | CONECT 2 3 37 | CONECT 2 4 38 | CONECT 4 5 39 | CONECT 5 6 40 | CONECT 5 7 41 | CONECT 1 8 42 | CONECT 1 9 43 | CONECT 1 10 44 | CONECT 2 11 45 | CONECT 3 12 46 | CONECT 3 13 47 | CONECT 3 14 48 | CONECT 4 15 49 | CONECT 5 16 50 | CONECT 6 17 51 | CONECT 6 18 52 | CONECT 6 19 53 | CONECT 7 20 54 | CONECT 7 21 55 | CONECT 7 22 56 | END 57 | -------------------------------------------------------------------------------- /Solvents/1-octanol/1-octanol.pdb: -------------------------------------------------------------------------------- 1 | TITLE 1-octanol 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.520 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.079 1.000 1.423 15 | ATOM 4 C03 MOL 1 -2.608 1.002 1.419 16 | ATOM 5 C04 MOL 1 -3.165 1.000 2.844 17 | ATOM 6 C05 MOL 1 -4.695 1.000 2.842 18 | ATOM 7 C06 MOL 1 -5.251 0.996 4.265 19 | ATOM 8 C07 MOL 1 -6.774 0.998 4.271 20 | ATOM 9 O08 MOL 1 -7.249 0.996 5.611 21 | ATOM 10 H09 MOL 1 1.378 0.999 -1.027 22 | ATOM 11 H0A MOL 1 1.391 0.112 0.507 23 | ATOM 12 H0B MOL 1 1.391 1.889 0.505 24 | ATOM 13 H0C MOL 1 -0.879 0.117 -0.541 25 | ATOM 14 H0D MOL 1 -0.879 1.883 -0.541 26 | ATOM 15 H0E MOL 1 -0.711 1.882 1.961 27 | ATOM 16 H0F MOL 1 -0.713 0.116 1.960 28 | ATOM 17 H0G MOL 1 -2.975 0.120 0.880 29 | ATOM 18 H0H MOL 1 -2.972 1.887 0.883 30 | ATOM 19 H0I MOL 1 -2.799 1.883 3.382 31 | ATOM 20 H0J MOL 1 -2.799 0.116 3.380 32 | ATOM 21 H0K MOL 1 -5.061 0.118 2.303 33 | ATOM 22 H0M MOL 1 -5.061 1.884 2.306 34 | ATOM 23 H0N MOL 1 -4.886 1.871 4.818 35 | ATOM 24 H0O MOL 1 -4.885 0.118 4.811 36 | ATOM 25 H0P MOL 1 -7.175 0.118 3.759 37 | ATOM 26 H0Q MOL 1 -7.164 1.893 3.776 38 | ATOM 27 H0R MOL 1 -6.912 0.191 6.039 39 | TER 40 | CONECT 1 2 41 | CONECT 2 3 42 | CONECT 3 4 43 | CONECT 4 5 44 | CONECT 5 6 45 | CONECT 6 7 46 | CONECT 7 8 47 | CONECT 8 9 48 | CONECT 1 10 49 | CONECT 1 11 50 | CONECT 1 12 51 | CONECT 2 13 52 | CONECT 2 14 53 | CONECT 3 15 54 | CONECT 3 16 55 | CONECT 4 17 56 | CONECT 4 18 57 | CONECT 5 19 58 | CONECT 5 20 59 | CONECT 6 21 60 | CONECT 6 22 61 | CONECT 7 23 62 | CONECT 7 24 63 | CONECT 8 25 64 | CONECT 8 26 65 | CONECT 9 27 66 | END 67 | -------------------------------------------------------------------------------- /Solvents/n-butylether/n-butylether.pdb: -------------------------------------------------------------------------------- 1 | TITLE n-butylether 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.519 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.085 1.000 1.419 15 | ATOM 4 C03 MOL 1 -2.609 1.002 1.402 16 | ATOM 5 O04 MOL 1 -3.089 1.003 2.747 17 | ATOM 6 C05 MOL 1 -4.516 1.007 2.783 18 | ATOM 7 C06 MOL 1 -4.975 1.010 4.236 19 | ATOM 8 C07 MOL 1 -6.499 1.016 4.332 20 | ATOM 9 C08 MOL 1 -6.974 1.018 5.776 21 | ATOM 10 H09 MOL 1 1.377 0.999 -1.028 22 | ATOM 11 H0A MOL 1 1.392 0.112 0.506 23 | ATOM 12 H0B MOL 1 1.392 1.889 0.504 24 | ATOM 13 H0C MOL 1 -0.877 0.117 -0.542 25 | ATOM 14 H0D MOL 1 -0.877 1.882 -0.543 26 | ATOM 15 H0E MOL 1 -0.725 1.876 1.973 27 | ATOM 16 H0F MOL 1 -0.727 0.122 1.972 28 | ATOM 17 H0G MOL 1 -2.980 0.109 0.886 29 | ATOM 18 H0H MOL 1 -2.978 1.895 0.885 30 | ATOM 19 H0I MOL 1 -4.894 0.114 2.271 31 | ATOM 20 H0J MOL 1 -4.890 1.900 2.268 32 | ATOM 21 H0K MOL 1 -4.557 1.886 4.748 33 | ATOM 22 H0M MOL 1 -4.563 0.133 4.751 34 | ATOM 23 H0N MOL 1 -6.905 0.134 3.822 35 | ATOM 24 H0O MOL 1 -6.898 1.900 3.821 36 | ATOM 25 H0P MOL 1 -6.619 0.129 6.306 37 | ATOM 26 H0Q MOL 1 -8.068 1.020 5.813 38 | ATOM 27 H0R MOL 1 -6.612 1.904 6.306 39 | TER 40 | CONECT 1 2 41 | CONECT 2 3 42 | CONECT 3 4 43 | CONECT 4 5 44 | CONECT 5 6 45 | CONECT 6 7 46 | CONECT 7 8 47 | CONECT 8 9 48 | CONECT 1 10 49 | CONECT 1 11 50 | CONECT 1 12 51 | CONECT 2 13 52 | CONECT 2 14 53 | CONECT 3 15 54 | CONECT 3 16 55 | CONECT 4 17 56 | CONECT 4 18 57 | CONECT 6 19 58 | CONECT 6 20 59 | CONECT 7 21 60 | CONECT 7 22 61 | CONECT 8 23 62 | CONECT 8 24 63 | CONECT 9 25 64 | CONECT 9 26 65 | CONECT 9 27 66 | END 67 | -------------------------------------------------------------------------------- /Solvents/methanol/methanol.itp: -------------------------------------------------------------------------------- 1 | ; methanol 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_803 H803 1.0080 0.000 A 2.50000E-01 1.25520E-01 18 | opls_800 C800 12.0110 -0.134 A 3.50000E-01 2.76144E-01 19 | opls_801 O801 15.9990 -0.616 A 3.12000E-01 7.11280E-01 20 | opls_805 H805 1.0080 0.381 A 0.00000E+00 0.00000E+00 21 | opls_802 H802 1.0080 0.123 A 2.50000E-01 1.25520E-01 22 | opls_804 H804 1.0080 0.000 A 2.50000E-01 1.25520E-01 23 | 24 | 25 | [ moleculetype ] 26 | ; name nrexcl 27 | MOL 3 28 | 29 | 30 | [ atoms ] 31 | ; nr type resnr residue atom cgnr charge mass 32 | 1 opls_800 1 MOL C00 1 -0.134 12.0110 33 | 2 opls_801 1 MOL O01 1 -0.616 15.9990 34 | 3 opls_802 1 MOL H02 1 0.123 1.0080 35 | 4 opls_802 1 MOL H03 1 0.123 1.0080 36 | 5 opls_802 1 MOL H04 1 0.123 1.0080 37 | 6 opls_805 1 MOL H05 1 0.381 1.0080 38 | 39 | 40 | [ bonds ] 41 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 42 | 2 1 1 0.1410 267776.000 43 | 3 1 1 0.1090 284512.000 44 | 4 1 1 0.1090 284512.000 45 | 5 1 1 0.1090 284512.000 46 | 6 2 1 0.0945 462750.400 47 | 48 | 49 | [ angles ] 50 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 51 | 2 1 3 1 109.500 292.880 52 | 2 1 4 1 109.500 292.880 53 | 2 1 5 1 109.500 292.880 54 | 1 2 6 1 108.500 460.240 55 | 3 1 4 1 107.800 276.144 56 | 3 1 5 1 107.800 276.144 57 | 4 1 5 1 107.800 276.144 58 | 59 | 60 | [ dihedrals ] 61 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 62 | 6 2 1 3 3 0.736 2.209 0.000 -2.946 -0.000 0.000 63 | 6 2 1 5 3 0.736 2.209 0.000 -2.946 -0.000 0.000 64 | 6 2 1 4 3 0.736 2.209 0.000 -2.946 -0.000 0.000 65 | 66 | 67 | -------------------------------------------------------------------------------- /Solvents/N-butyl-1-butanamine/N-butyl-1-butanamine.pdb: -------------------------------------------------------------------------------- 1 | TITLE N-butyl-1-butanamine 2 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 3 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 4 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 5 | REMARK doi: 10.1021/acs.jctc.1c00047. 6 | REMARK 7 | REMARK GAML charges with OPLS-AA 8 | REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 9 | REMARK Jorgensen Lab @ Yale University 10 | REMARK 11 | REMARK GROMACS 5.0.7 is recommended for the values given below 12 | ATOM 1 C00 MOL 1 1.000 1.000 0.000 13 | ATOM 2 C01 MOL 1 -0.520 1.000 0.000 14 | ATOM 3 C02 MOL 1 -1.082 1.000 1.423 15 | ATOM 4 C03 MOL 1 -2.612 0.998 1.408 16 | ATOM 5 N04 MOL 1 -3.123 0.996 2.779 17 | ATOM 6 C05 MOL 1 -4.586 0.996 2.790 18 | ATOM 7 C06 MOL 1 -5.096 0.996 4.232 19 | ATOM 8 C07 MOL 1 -6.625 0.995 4.273 20 | ATOM 9 C08 MOL 1 -7.146 0.993 5.701 21 | ATOM 10 H09 MOL 1 1.378 1.001 -1.027 22 | ATOM 11 H0A MOL 1 1.391 0.111 0.505 23 | ATOM 12 H0B MOL 1 1.391 1.888 0.507 24 | ATOM 13 H0C MOL 1 -0.879 0.117 -0.542 25 | ATOM 14 H0D MOL 1 -0.879 1.883 -0.542 26 | ATOM 15 H0E MOL 1 -0.715 1.884 1.960 27 | ATOM 16 H0F MOL 1 -0.714 0.117 1.961 28 | ATOM 17 H0G MOL 1 -2.967 0.107 0.876 29 | ATOM 18 H0H MOL 1 -2.972 1.883 0.870 30 | ATOM 19 H0I MOL 1 -2.776 1.818 3.274 31 | ATOM 20 H0J MOL 1 -4.962 0.105 2.273 32 | ATOM 21 H0K MOL 1 -4.969 1.882 2.267 33 | ATOM 22 H0M MOL 1 -4.718 1.881 4.761 34 | ATOM 23 H0N MOL 1 -4.715 0.113 4.761 35 | ATOM 24 H0O MOL 1 -7.009 0.112 3.749 36 | ATOM 25 H0P MOL 1 -7.011 1.878 3.751 37 | ATOM 26 H0Q MOL 1 -6.803 0.105 6.242 38 | ATOM 27 H0R MOL 1 -8.240 0.991 5.704 39 | ATOM 28 H0S MOL 1 -6.803 1.879 6.244 40 | TER 41 | CONECT 1 2 42 | CONECT 2 3 43 | CONECT 3 4 44 | CONECT 4 5 45 | CONECT 5 6 46 | CONECT 6 7 47 | CONECT 7 8 48 | CONECT 8 9 49 | CONECT 1 10 50 | CONECT 1 11 51 | CONECT 1 12 52 | CONECT 2 13 53 | CONECT 2 14 54 | CONECT 3 15 55 | CONECT 3 16 56 | CONECT 4 17 57 | CONECT 4 18 58 | CONECT 5 19 59 | CONECT 6 20 60 | CONECT 6 21 61 | CONECT 7 22 62 | CONECT 7 23 63 | CONECT 8 24 64 | CONECT 8 25 65 | CONECT 9 26 66 | CONECT 9 27 67 | CONECT 9 28 68 | END 69 | -------------------------------------------------------------------------------- /GAML/function_gen_range.py: -------------------------------------------------------------------------------- 1 | import random 2 | 3 | 4 | def func_gen_range(rlist,percent=0.8): 5 | """filtering charge range 6 | 7 | For an integer 1D list, start from the mode number, find 8 | a surrounding range, which contains data points no less 9 | than certain percent 10 | 11 | For return value, the ndxmin is included in the range, 12 | while ndxmax is not 13 | 14 | Returns: 15 | int : lower-bound 16 | int : higher-bound 17 | """ 18 | try: 19 | if not isinstance(rlist,list): 20 | raise ValueError 21 | else: 22 | for i in rlist: 23 | if not isinstance(i,int): 24 | raise ValueError 25 | percent = float(percent) 26 | if percent <= 0 or percent > 1: 27 | raise ValueError 28 | except ValueError: 29 | raise ValueError('rlist: 1D integer list; percent: between 0 & 1') 30 | 31 | lth = len(rlist) 32 | rmax = max(rlist) 33 | ndxlist = [] 34 | for i in range(lth): 35 | if rlist[i] == rmax: 36 | ndxlist.append(i) 37 | 38 | i = 1 39 | while i < len(ndxlist): 40 | if ndxlist[i] - ndxlist[i-1] == 1: 41 | ndxlist.remove(ndxlist[i-1]) 42 | else: 43 | i += 1 44 | 45 | chooselist = [] 46 | total_sum = sum(rlist) 47 | rsum = [] 48 | for ndxmax in ndxlist: 49 | 50 | ndxmin = ndxmax 51 | 52 | while True: 53 | if rlist[ndxmin] < rlist[ndxmax]: 54 | if ndxmax + 1 < lth: 55 | ndxmax = ndxmax + 1 56 | elif ndxmax == lth - 1: 57 | if ndxmin - 1 > 0: 58 | ndxmin = ndxmin - 1 59 | else: 60 | ndxmin = 0 61 | else: 62 | ndxmax = lth - 1 63 | 64 | else: 65 | if ndxmin - 1 > 0 : 66 | ndxmin = ndxmin - 1 67 | elif ndxmin == 0: 68 | if ndxmax + 1 < lth: 69 | ndxmax = ndxmax + 1 70 | else: 71 | ndxmax = lth - 1 72 | else: 73 | ndxmin = 0 74 | 75 | lsum = sum(rlist[ndxmin:ndxmax+1]) 76 | 77 | if lsum / total_sum >= percent: 78 | ltmp = [] 79 | ltmp.append(ndxmin) 80 | ltmp.append(ndxmax+1) 81 | rsum.append(lsum) 82 | chooselist.append(ltmp) 83 | break 84 | 85 | if len(chooselist) >= 2: 86 | ndxlist = [] 87 | for i in range(len(rsum)): 88 | if rsum[i] == max(rsum): 89 | ndxlist.append(i) 90 | 91 | choose = random.randrange(len(ndxlist)) 92 | 93 | ndxmin = chooselist[choose][0] 94 | ndxmax = chooselist[choose][1] 95 | 96 | return ndxmin,ndxmax 97 | 98 | 99 | 100 | -------------------------------------------------------------------------------- /GAML/file_gen_scripts.py: -------------------------------------------------------------------------------- 1 | """Get pre-defined script files 2 | """ 3 | from GAML.functions import file_gen_new 4 | import os 5 | import shutil 6 | from pkg_resources import resource_listdir, resource_filename 7 | 8 | 9 | class File_gen_scripts: 10 | def __init__(self,*args,**kwargs): 11 | self.n = None 12 | if 'number' in kwargs and kwargs['number'] is not None: 13 | try: 14 | self.n = int(float(kwargs['number'])) 15 | except ValueError: 16 | self.available = True 17 | print('Error: wrong choose') 18 | 19 | self.files = resource_listdir(__name__,'scripts/') 20 | # remove python cache folder 21 | if '__pycache__' in self.files: self.files.remove('__pycache__') 22 | 23 | self.available = True 24 | if self.n is not None and self.n <= len(files): self.available = False 25 | 26 | 27 | 28 | def run(self): 29 | """get built-in script file""" 30 | details = { 31 | 'bash_analysesDES.sh' : 'For DES result analyses', 32 | 'bash_DES.sh' : 'For DES training', 33 | 'bash_GAML.sh' : 'For conventional solvents training', 34 | 'bash_genTopfiles.sh' : 'For GROMACS topology file generations', 35 | 'bash_rmfilesIndividual.sh': 'For folder cleanup', 36 | 'bash_visAdd.sh' : 'For viscosity property training', 37 | 'bash_visAnalysisByFolder.sh': 'For viscosity property analyzing', 38 | 'GAML-BASH-Interface.sh': 'For command GAML_autotrain', 39 | 'py_bool_repeatsChk.py' : 'For charge pair repeats check out', 40 | } 41 | 42 | if self.available: 43 | print('Available scripts:') 44 | for cnt,f in enumerate(self.files): 45 | if f in details: 46 | print(' {:2d} --> {:<30} {:}'.format(cnt+1,f,details[f])) 47 | else: 48 | print(' {:2d} --> {:}'.format(cnt+1,f)) 49 | print('\nWhich scripts do you want to get?') 50 | print('Please input its number. (Input q/quit to quit)') 51 | while True: 52 | tmp = input() 53 | if tmp.lower() in ['q','quit']: break 54 | try: 55 | self.n = int(float(tmp)) 56 | if self.n <= 0: 57 | self.n = None 58 | raise ValueError 59 | except ValueError: 60 | pass 61 | if isinstance(self.n,int) and self.n <= len(self.files): 62 | self.available = False 63 | break 64 | else: 65 | print('Wrong choose. (Input q/quit to quit)') 66 | 67 | if self.available: 68 | print('You decided to quit..') 69 | else: 70 | cwd = os.getcwd() 71 | fname = self.files[self.n-1] 72 | fp = resource_filename(__name__,'scripts/'+fname) 73 | if os.path.isfile(fp): 74 | fname = file_gen_new(fname) 75 | print('Note: script file: < {:} >'.format(fname)) 76 | shutil.copy(fp,cwd+'/'+fname) 77 | 78 | 79 | 80 | def file_print(self): 81 | """place holder""" 82 | pass 83 | 84 | 85 | 86 | -------------------------------------------------------------------------------- /Solvents/acetaldehyde/acetaldehyde.itp: -------------------------------------------------------------------------------- 1 | ; acetaldehyde 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_803 H803 1.0080 0.273 A 2.50000E-01 1.25520E-01 18 | opls_800 C800 12.0110 -0.63 A 3.50000E-01 2.76144E-01 19 | opls_802 O802 15.9990 -0.146 A 2.96000E-01 8.78640E-01 20 | opls_804 H804 1.0080 0.000 A 2.50000E-01 1.25520E-01 21 | opls_805 H805 1.0080 0.000 A 2.50000E-01 1.25520E-01 22 | opls_806 H806 1.0080 0.028 A 2.50000E-01 1.25520E-01 23 | opls_801 C801 12.0110 -0.071 A 3.55000E-01 2.92880E-01 24 | 25 | 26 | [ moleculetype ] 27 | ; name nrexcl 28 | MOL 3 29 | 30 | 31 | [ atoms ] 32 | ; nr type resnr residue atom cgnr charge mass 33 | 1 opls_800 1 MOL C00 1 -0.63 12.0110 34 | 2 opls_801 1 MOL C01 1 -0.071 12.0110 35 | 3 opls_802 1 MOL O02 1 -0.146 15.9990 36 | 4 opls_803 1 MOL H03 1 0.273 1.0080 37 | 5 opls_803 1 MOL H04 1 0.273 1.0080 38 | 6 opls_803 1 MOL H05 1 0.273 1.0080 39 | 7 opls_806 1 MOL H06 1 0.028 1.0080 40 | 41 | 42 | [ bonds ] 43 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 44 | 2 1 1 0.1522 265265.600 45 | 3 2 1 0.1229 476976.000 46 | 4 1 1 0.1090 284512.000 47 | 5 1 1 0.1090 284512.000 48 | 6 1 1 0.1090 284512.000 49 | 7 2 1 0.1090 284512.000 50 | 51 | 52 | [ angles ] 53 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 54 | 1 2 3 1 120.400 669.440 55 | 2 1 4 1 109.500 292.880 56 | 2 1 5 1 109.500 292.880 57 | 2 1 6 1 109.500 292.880 58 | 1 2 7 1 115.000 292.880 59 | 4 1 5 1 107.800 276.144 60 | 5 1 6 1 107.800 276.144 61 | 3 2 7 1 123.000 292.880 62 | 4 1 6 1 107.800 276.144 63 | 64 | 65 | [ dihedrals ] 66 | ; IMPROPER DIHEDRAL ANGLES 67 | ; ai aj ak al func deg k(kj mol-1) mp 68 | 7 2 1 3 4 180.000 43.932 2 69 | 70 | 71 | [ dihedrals ] 72 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 73 | 7 2 1 5 3 0.753 2.259 0.000 -3.012 -0.000 0.000 74 | 7 2 1 6 3 0.753 2.259 0.000 -3.012 -0.000 0.000 75 | 7 2 1 4 3 0.753 2.259 0.000 -3.012 -0.000 0.000 76 | 4 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 77 | 5 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 78 | 6 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 79 | 80 | 81 | -------------------------------------------------------------------------------- /Solvents/nitromethane/nitromethane.itp: -------------------------------------------------------------------------------- 1 | ; nitromethane 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_801 N801 14.0070 0.695 A 3.25000E-01 5.02080E-01 18 | opls_800 C800 12.0110 -0.475 A 3.50000E-01 2.76144E-01 19 | opls_804 H804 1.0080 0.182 A 2.50000E-01 1.25520E-01 20 | opls_802 O802 15.9990 -0.383 A 2.96000E-01 7.11280E-01 21 | opls_805 H805 1.0080 0.000 A 2.50000E-01 1.25520E-01 22 | opls_803 O803 15.9990 0.000 A 2.96000E-01 7.11280E-01 23 | opls_806 H806 1.0080 0.000 A 2.50000E-01 1.25520E-01 24 | 25 | 26 | [ moleculetype ] 27 | ; name nrexcl 28 | MOL 3 29 | 30 | 31 | [ atoms ] 32 | ; nr type resnr residue atom cgnr charge mass 33 | 1 opls_800 1 MOL C00 1 -0.475 12.0110 34 | 2 opls_801 1 MOL N01 1 0.695 14.0070 35 | 3 opls_802 1 MOL O02 1 -0.383 15.9990 36 | 4 opls_802 1 MOL O03 1 -0.383 15.9990 37 | 5 opls_804 1 MOL H04 1 0.182 1.0080 38 | 6 opls_804 1 MOL H05 1 0.182 1.0080 39 | 7 opls_804 1 MOL H06 1 0.182 1.0080 40 | 41 | 42 | [ bonds ] 43 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 44 | 2 1 1 0.1490 313800.000 45 | 3 2 1 0.1225 460240.000 46 | 4 2 1 0.1225 460240.000 47 | 5 1 1 0.1090 284512.000 48 | 6 1 1 0.1090 284512.000 49 | 7 1 1 0.1090 284512.000 50 | 51 | 52 | [ angles ] 53 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 54 | 1 2 3 1 117.500 669.440 55 | 1 2 4 1 117.500 669.440 56 | 2 1 5 1 105.000 292.880 57 | 2 1 6 1 105.000 292.880 58 | 2 1 7 1 105.000 292.880 59 | 6 1 7 1 107.800 276.144 60 | 5 1 6 1 107.800 276.144 61 | 3 2 4 1 125.000 669.440 62 | 5 1 7 1 107.800 276.144 63 | 64 | 65 | [ dihedrals ] 66 | ; IMPROPER DIHEDRAL ANGLES 67 | ; ai aj ak al func deg k(kj mol-1) mp 68 | 4 2 1 3 4 180.000 10.460 2 69 | 70 | 71 | [ dihedrals ] 72 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 73 | 5 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 74 | 5 1 2 4 3 0.000 0.000 0.000 -0.000 -0.000 0.000 75 | 6 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 76 | 7 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 77 | 6 1 2 4 3 0.000 0.000 0.000 -0.000 -0.000 0.000 78 | 7 1 2 4 3 0.000 0.000 0.000 -0.000 -0.000 0.000 79 | 80 | 81 | -------------------------------------------------------------------------------- /GAML/main.py: -------------------------------------------------------------------------------- 1 | from GAML.charge_gen_range import Charge_gen_range 2 | from GAML.charge_gen_scheme import Charge_gen_scheme 3 | from GAML.file_gen_gaussian import File_gen_gaussian 4 | from GAML.file_gen_gromacstop import File_gen_gromacstop 5 | from GAML.gaml import GAML 6 | from GAML.file_gen_mdpotential import File_gen_mdpotential 7 | from GAML.gaml_autotrain import GAML_autotrain 8 | from GAML.fss_analysis import FSS_analysis 9 | from GAML.parsecmd import parsecmd 10 | from GAML.parsefile import parsefile 11 | from GAML.defaults import parlist 12 | from GAML.file_gen_scripts import File_gen_scripts 13 | 14 | import sys 15 | from sys import exit 16 | 17 | 18 | def run(fdict): 19 | """Execute command 20 | 21 | assumes input directory has been properly processed. 22 | 23 | This method should be updated for future updates 24 | """ 25 | cmd = fdict['command'] 26 | if cmd == 'file_gen_gaussian': 27 | fp = File_gen_gaussian(**fdict) 28 | elif cmd == 'gaml_autotrain': 29 | fp = GAML_autotrain(**fdict) 30 | elif cmd == 'charge_gen_range': 31 | fp = Charge_gen_range(**fdict) 32 | elif cmd == 'charge_gen_scheme': 33 | fp = Charge_gen_scheme(**fdict) 34 | elif cmd == 'file_gen_gromacstop': 35 | fp = File_gen_gromacstop(**fdict) 36 | elif cmd == 'gaml': 37 | fp = GAML(**fdict) 38 | elif cmd == 'fss_analysis': 39 | fp = FSS_analysis(**fdict) 40 | elif cmd == 'file_gen_mdpotential': 41 | fp = File_gen_mdpotential(**fdict) 42 | elif cmd == 'file_gen_scripts': 43 | fp = File_gen_scripts(**fdict) 44 | else: 45 | # Normally, this part will never be executed. 46 | # However, it is still defined 47 | print('Error: no command is executed') 48 | exit() 49 | 50 | fp.run() 51 | fp.file_print() 52 | 53 | 54 | 55 | def cmd_line_runner(): 56 | cmdlist = [i['command'].lower() for i in parlist] 57 | 58 | if len(sys.argv) == 1: 59 | print('GAML package\n\n') 60 | print('Option 1, using setting file:\ngaml settingfile\n\n') 61 | print('Option 2, using command line:\n') 62 | s,t = parsecmd('') 63 | exit() 64 | 65 | if sys.argv[1].lower() in ['-v','--version','-h','--help',*cmdlist]: 66 | log, args = parsecmd(sys.argv[1:]) 67 | if log['nice']: 68 | for fdict in parlist: 69 | if fdict['command'] == args['command'].lower(): 70 | for key in args: 71 | if args[key] is not None: 72 | fdict[key] = args[key] 73 | run(fdict) 74 | else: 75 | print(log['info']) 76 | exit() 77 | else: 78 | log, profile = parsefile(sys.argv[1]) 79 | if not log['nice']: 80 | print(log['info']) 81 | exit() 82 | 83 | for block in profile: 84 | for i in block: 85 | if i[0] == 'command': 86 | cmd = i[1] 87 | break 88 | 89 | for fdict in parlist: 90 | if fdict['command'] == cmd.lower(): 91 | for ndx in block: 92 | if ndx[0] in fdict: 93 | fdict[ndx[0]] = ndx[1] 94 | else: 95 | print('Error: ',ndx[2]) 96 | exit() 97 | run(fdict) 98 | 99 | 100 | 101 | if __name__ == '__main__': 102 | cmd_line_runner() 103 | 104 | 105 | 106 | -------------------------------------------------------------------------------- /Solvents/methylformate/methylformate.itp: -------------------------------------------------------------------------------- 1 | ; methylformate 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_803 O803 15.9990 -0.132 A 2.96000E-01 8.78640E-01 18 | opls_800 C800 12.0110 -0.219 A 3.50000E-01 2.76144E-01 19 | opls_807 H807 1.0080 0.3 A 2.50000E-01 1.25520E-01 20 | opls_804 H804 1.0080 0.042 A 2.50000E-01 1.25520E-01 21 | opls_802 C802 12.0110 0.048 A 3.55000E-01 2.92880E-01 22 | opls_805 H805 1.0080 0.000 A 2.50000E-01 1.25520E-01 23 | opls_806 H806 1.0080 0.000 A 2.50000E-01 1.25520E-01 24 | opls_801 O801 15.9990 -0.123 A 2.90000E-01 5.85760E-01 25 | 26 | 27 | [ moleculetype ] 28 | ; name nrexcl 29 | MOL 3 30 | 31 | 32 | [ atoms ] 33 | ; nr type resnr residue atom cgnr charge mass 34 | 1 opls_800 1 MOL C00 1 -0.219 12.0110 35 | 2 opls_801 1 MOL O01 1 -0.123 15.9990 36 | 3 opls_802 1 MOL C02 1 0.048 12.0110 37 | 4 opls_803 1 MOL O03 1 -0.132 15.9990 38 | 5 opls_804 1 MOL H04 1 0.042 1.0080 39 | 6 opls_804 1 MOL H05 1 0.042 1.0080 40 | 7 opls_804 1 MOL H06 1 0.042 1.0080 41 | 8 opls_807 1 MOL H07 1 0.3 1.0080 42 | 43 | 44 | [ bonds ] 45 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 46 | 2 1 1 0.1410 267776.000 47 | 3 2 1 0.1327 179075.200 48 | 4 3 1 0.1229 476976.000 49 | 5 1 1 0.1090 284512.000 50 | 6 1 1 0.1090 284512.000 51 | 7 1 1 0.1090 284512.000 52 | 8 3 1 0.1090 284512.000 53 | 54 | 55 | [ angles ] 56 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 57 | 1 2 3 1 116.900 694.544 58 | 2 3 4 1 123.400 694.544 59 | 2 1 5 1 109.500 292.880 60 | 2 1 6 1 109.500 292.880 61 | 2 1 7 1 109.500 292.880 62 | 2 3 8 1 115.000 334.720 63 | 6 1 7 1 107.800 276.144 64 | 4 3 8 1 123.000 292.880 65 | 5 1 6 1 107.800 276.144 66 | 5 1 7 1 107.800 276.144 67 | 68 | 69 | [ dihedrals ] 70 | ; IMPROPER DIHEDRAL ANGLES 71 | ; ai aj ak al func deg k(kj mol-1) mp 72 | 8 3 2 4 4 180.000 43.932 2 73 | 74 | 75 | [ dihedrals ] 76 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 77 | 8 3 2 1 3 31.206 -9.768 -21.439 -0.000 -0.000 0.000 78 | 5 1 2 3 3 0.414 1.243 0.000 -1.657 -0.000 0.000 79 | 6 1 2 3 3 0.414 1.243 0.000 -1.657 -0.000 0.000 80 | 7 1 2 3 3 0.414 1.243 0.000 -1.657 -0.000 0.000 81 | 4 3 2 1 3 21.439 0.000 -21.439 -0.000 -0.000 0.000 82 | 83 | 84 | -------------------------------------------------------------------------------- /Solvents/dimethylether/dimethylether.itp: -------------------------------------------------------------------------------- 1 | ; dimethylether 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_803 H803 1.0080 0.214 A 2.50000E-01 1.25520E-01 18 | opls_802 C802 12.0110 0.000 A 3.50000E-01 2.76144E-01 19 | opls_808 H808 1.0080 0.000 A 2.50000E-01 1.25520E-01 20 | opls_800 C800 12.0110 -0.639 A 3.50000E-01 2.76144E-01 21 | opls_807 H807 1.0080 0.000 A 2.50000E-01 1.25520E-01 22 | opls_804 H804 1.0080 0.000 A 2.50000E-01 1.25520E-01 23 | opls_805 H805 1.0080 0.000 A 2.50000E-01 1.25520E-01 24 | opls_806 H806 1.0080 0.000 A 2.50000E-01 1.25520E-01 25 | opls_801 O801 15.9990 -0.006 A 2.90000E-01 5.85760E-01 26 | 27 | 28 | [ moleculetype ] 29 | ; name nrexcl 30 | MOL 3 31 | 32 | 33 | [ atoms ] 34 | ; nr type resnr residue atom cgnr charge mass 35 | 1 opls_800 1 MOL C00 1 -0.639 12.0110 36 | 2 opls_801 1 MOL O01 1 -0.006 15.9990 37 | 3 opls_800 1 MOL C02 1 -0.639 12.0110 38 | 4 opls_803 1 MOL H03 1 0.214 1.0080 39 | 5 opls_803 1 MOL H04 1 0.214 1.0080 40 | 6 opls_803 1 MOL H05 1 0.214 1.0080 41 | 7 opls_803 1 MOL H06 1 0.214 1.0080 42 | 8 opls_803 1 MOL H07 1 0.214 1.0080 43 | 9 opls_803 1 MOL H08 1 0.214 1.0080 44 | 45 | 46 | [ bonds ] 47 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 48 | 2 1 1 0.1410 267776.000 49 | 3 2 1 0.1410 267776.000 50 | 4 1 1 0.1090 284512.000 51 | 5 1 1 0.1090 284512.000 52 | 6 1 1 0.1090 284512.000 53 | 7 3 1 0.1090 284512.000 54 | 8 3 1 0.1090 284512.000 55 | 9 3 1 0.1090 284512.000 56 | 57 | 58 | [ angles ] 59 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 60 | 1 2 3 1 109.500 502.080 61 | 2 1 4 1 109.500 292.880 62 | 2 1 5 1 109.500 292.880 63 | 2 1 6 1 109.500 292.880 64 | 2 3 7 1 109.500 292.880 65 | 2 3 8 1 109.500 292.880 66 | 2 3 9 1 109.500 292.880 67 | 4 1 5 1 107.800 276.144 68 | 5 1 6 1 107.800 276.144 69 | 7 3 8 1 107.800 276.144 70 | 8 3 9 1 107.800 276.144 71 | 4 1 6 1 107.800 276.144 72 | 7 3 9 1 107.800 276.144 73 | 74 | 75 | [ dihedrals ] 76 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 77 | 4 1 2 3 3 1.590 4.770 0.000 -6.360 -0.000 0.000 78 | 7 3 2 1 3 1.590 4.770 0.000 -6.360 -0.000 0.000 79 | 5 1 2 3 3 1.590 4.770 0.000 -6.360 -0.000 0.000 80 | 8 3 2 1 3 1.590 4.770 0.000 -6.360 -0.000 0.000 81 | 9 3 2 1 3 1.590 4.770 0.000 -6.360 -0.000 0.000 82 | 6 1 2 3 3 1.590 4.770 0.000 -6.360 -0.000 0.000 83 | 84 | 85 | -------------------------------------------------------------------------------- /Solvents/dimethylsulfide/dimethylsulfide.itp: -------------------------------------------------------------------------------- 1 | ; dimethylsulfide 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_803 H803 1.0080 0.185 A 2.50000E-01 1.25520E-01 18 | opls_802 C802 12.0110 0.000 A 3.50000E-01 2.76144E-01 19 | opls_808 H808 1.0080 0.000 A 2.50000E-01 1.25520E-01 20 | opls_800 C800 12.0110 -0.506 A 3.50000E-01 2.76144E-01 21 | opls_807 H807 1.0080 0.000 A 2.50000E-01 1.25520E-01 22 | opls_804 H804 1.0080 0.000 A 2.50000E-01 1.25520E-01 23 | opls_801 S801 32.0600 -0.098 A 3.60000E-01 1.48532E+00 24 | opls_805 H805 1.0080 0.000 A 2.50000E-01 1.25520E-01 25 | opls_806 H806 1.0080 0.000 A 2.50000E-01 1.25520E-01 26 | 27 | 28 | [ moleculetype ] 29 | ; name nrexcl 30 | MOL 3 31 | 32 | 33 | [ atoms ] 34 | ; nr type resnr residue atom cgnr charge mass 35 | 1 opls_800 1 MOL C00 1 -0.506 12.0110 36 | 2 opls_801 1 MOL S01 1 -0.098 32.0600 37 | 3 opls_800 1 MOL C02 1 -0.506 12.0110 38 | 4 opls_803 1 MOL H03 1 0.185 1.0080 39 | 5 opls_803 1 MOL H04 1 0.185 1.0080 40 | 6 opls_803 1 MOL H05 1 0.185 1.0080 41 | 7 opls_803 1 MOL H06 1 0.185 1.0080 42 | 8 opls_803 1 MOL H07 1 0.185 1.0080 43 | 9 opls_803 1 MOL H08 1 0.185 1.0080 44 | 45 | 46 | [ bonds ] 47 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 48 | 2 1 1 0.1810 185769.600 49 | 3 2 1 0.1810 185769.600 50 | 4 1 1 0.1090 284512.000 51 | 5 1 1 0.1090 284512.000 52 | 6 1 1 0.1090 284512.000 53 | 7 3 1 0.1090 284512.000 54 | 8 3 1 0.1090 284512.000 55 | 9 3 1 0.1090 284512.000 56 | 57 | 58 | [ angles ] 59 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 60 | 1 2 3 1 98.900 518.816 61 | 2 1 4 1 109.500 292.880 62 | 2 1 5 1 109.500 292.880 63 | 2 1 6 1 109.500 292.880 64 | 2 3 7 1 109.500 292.880 65 | 2 3 8 1 109.500 292.880 66 | 2 3 9 1 109.500 292.880 67 | 4 1 5 1 107.800 276.144 68 | 5 1 6 1 107.800 276.144 69 | 7 3 8 1 107.800 276.144 70 | 8 3 9 1 107.800 276.144 71 | 4 1 6 1 107.800 276.144 72 | 7 3 9 1 107.800 276.144 73 | 74 | 75 | [ dihedrals ] 76 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 77 | 4 1 2 3 3 1.354 4.061 0.000 -5.414 -0.000 0.000 78 | 7 3 2 1 3 1.354 4.061 0.000 -5.414 -0.000 0.000 79 | 5 1 2 3 3 1.354 4.061 0.000 -5.414 -0.000 0.000 80 | 8 3 2 1 3 1.354 4.061 0.000 -5.414 -0.000 0.000 81 | 9 3 2 1 3 1.354 4.061 0.000 -5.414 -0.000 0.000 82 | 6 1 2 3 3 1.354 4.061 0.000 -5.414 -0.000 0.000 83 | 84 | 85 | -------------------------------------------------------------------------------- /Solvents/aceticAcid/aceticAcid.itp: -------------------------------------------------------------------------------- 1 | ; aceticAcid 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_800 C800 12.0110 -0.484 A 3.50000E-01 2.76144E-01 18 | opls_802 O802 15.9990 -0.105 A 2.96000E-01 8.78640E-01 19 | opls_804 H804 1.0080 0.234 A 2.50000E-01 1.25520E-01 20 | opls_803 O803 15.9990 -0.508 A 3.12000E-01 7.11280E-01 21 | opls_807 H807 1.0080 0.266 A 0.00000E+00 0.00000E+00 22 | opls_805 H805 1.0080 0.000 A 2.50000E-01 1.25520E-01 23 | opls_806 H806 1.0080 0.000 A 2.50000E-01 1.25520E-01 24 | opls_801 C801 12.0110 0.129 A 3.55000E-01 2.92880E-01 25 | 26 | 27 | [ moleculetype ] 28 | ; name nrexcl 29 | MOL 3 30 | 31 | 32 | [ atoms ] 33 | ; nr type resnr residue atom cgnr charge mass 34 | 1 opls_800 1 MOL C00 1 -0.484 12.0110 35 | 2 opls_801 1 MOL C01 1 0.129 12.0110 36 | 3 opls_802 1 MOL O02 1 -0.105 15.9990 37 | 4 opls_803 1 MOL O03 1 -0.508 15.9990 38 | 5 opls_804 1 MOL H04 1 0.234 1.0080 39 | 6 opls_804 1 MOL H05 1 0.234 1.0080 40 | 7 opls_804 1 MOL H06 1 0.234 1.0080 41 | 8 opls_807 1 MOL H07 1 0.266 1.0080 42 | 43 | 44 | [ bonds ] 45 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 46 | 2 1 1 0.1522 265265.600 47 | 3 2 1 0.1229 476976.000 48 | 4 2 1 0.1364 376560.000 49 | 5 1 1 0.1090 284512.000 50 | 6 1 1 0.1090 284512.000 51 | 7 1 1 0.1090 284512.000 52 | 8 4 1 0.0945 462750.400 53 | 54 | 55 | [ angles ] 56 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 57 | 1 2 3 1 120.400 669.440 58 | 1 2 4 1 108.000 585.760 59 | 2 1 5 1 109.500 292.880 60 | 2 1 6 1 109.500 292.880 61 | 2 1 7 1 109.500 292.880 62 | 2 4 8 1 113.000 292.880 63 | 6 1 7 1 107.800 276.144 64 | 5 1 6 1 107.800 276.144 65 | 3 2 4 1 121.000 669.440 66 | 5 1 7 1 107.800 276.144 67 | 68 | 69 | [ dihedrals ] 70 | ; IMPROPER DIHEDRAL ANGLES 71 | ; ai aj ak al func deg k(kj mol-1) mp 72 | 4 2 1 3 4 180.000 43.932 2 73 | 74 | 75 | [ dihedrals ] 76 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 77 | 5 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 78 | 7 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 79 | 6 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 80 | 5 1 2 4 3 0.000 0.000 0.000 -0.000 -0.000 0.000 81 | 6 1 2 4 3 0.000 0.000 0.000 -0.000 -0.000 0.000 82 | 7 1 2 4 3 0.000 0.000 0.000 -0.000 -0.000 0.000 83 | 8 4 2 1 3 26.150 -3.138 -23.012 -0.000 -0.000 0.000 84 | 8 4 2 3 3 23.012 0.000 -23.012 -0.000 -0.000 0.000 85 | 86 | 87 | -------------------------------------------------------------------------------- /Solvents/bromoethane/bromoethane.itp: -------------------------------------------------------------------------------- 1 | ; bromoethane 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_803 H803 1.0080 0.122 A 2.50000E-01 1.25520E-01 18 | opls_802 Br802 79.9040 -0.107 A 3.47000E-01 1.96648E+00 19 | opls_800 C800 12.0110 -0.424 A 3.50000E-01 2.76144E-01 20 | opls_801 C801 12.0110 -0.117 A 3.50000E-01 2.76144E-01 21 | opls_807 H807 1.0080 0.000 A 2.50000E-01 1.25520E-01 22 | opls_804 H804 1.0080 0.000 A 2.50000E-01 1.25520E-01 23 | opls_805 H805 1.0080 0.000 A 2.50000E-01 1.25520E-01 24 | opls_806 H806 1.0080 0.141 A 2.50000E-01 1.25520E-01 25 | 26 | 27 | [ moleculetype ] 28 | ; name nrexcl 29 | MOL 3 30 | 31 | 32 | [ atoms ] 33 | ; nr type resnr residue atom cgnr charge mass 34 | 1 opls_800 1 MOL C00 1 -0.424 12.0110 35 | 2 opls_801 1 MOL C01 1 -0.117 12.0110 36 | 3 opls_802 1 MOL Br2 1 -0.107 79.9040 37 | 4 opls_803 1 MOL H03 1 0.122 1.0080 38 | 5 opls_803 1 MOL H04 1 0.122 1.0080 39 | 6 opls_803 1 MOL H05 1 0.122 1.0080 40 | 7 opls_806 1 MOL H06 1 0.141 1.0080 41 | 8 opls_806 1 MOL H07 1 0.141 1.0080 42 | 43 | 44 | [ bonds ] 45 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 46 | 2 1 1 0.1529 224262.400 47 | 3 2 1 0.1945 205016.000 48 | 4 1 1 0.1090 284512.000 49 | 5 1 1 0.1090 284512.000 50 | 6 1 1 0.1090 284512.000 51 | 7 2 1 0.1090 284512.000 52 | 8 2 1 0.1090 284512.000 53 | 54 | 55 | [ angles ] 56 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 57 | 1 2 3 1 110.000 577.392 58 | 2 1 4 1 110.700 313.800 59 | 2 1 5 1 110.700 313.800 60 | 2 1 6 1 110.700 313.800 61 | 1 2 7 1 110.700 313.800 62 | 1 2 8 1 110.700 313.800 63 | 4 1 5 1 107.800 276.144 64 | 5 1 6 1 107.800 276.144 65 | 3 2 7 1 107.600 426.768 66 | 3 2 8 1 107.600 426.768 67 | 4 1 6 1 107.800 276.144 68 | 7 2 8 1 107.800 276.144 69 | 70 | 71 | [ dihedrals ] 72 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 73 | 4 1 2 3 3 0.837 2.510 0.000 -3.347 -0.000 0.000 74 | 5 1 2 3 3 0.837 2.510 0.000 -3.347 -0.000 0.000 75 | 6 1 2 3 3 0.837 2.510 0.000 -3.347 -0.000 0.000 76 | 8 2 1 6 3 0.628 1.883 0.000 -2.510 -0.000 0.000 77 | 7 2 1 5 3 0.628 1.883 0.000 -2.510 -0.000 0.000 78 | 8 2 1 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 79 | 8 2 1 5 3 0.628 1.883 0.000 -2.510 -0.000 0.000 80 | 7 2 1 6 3 0.628 1.883 0.000 -2.510 -0.000 0.000 81 | 7 2 1 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 82 | 83 | 84 | -------------------------------------------------------------------------------- /Solvents/ethylchloride/ethylchloride.itp: -------------------------------------------------------------------------------- 1 | ; ethylchloride 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_803 H803 1.0080 0.124 A 2.50000E-01 1.25520E-01 18 | opls_800 C800 12.0110 -0.488 A 3.50000E-01 2.76144E-01 19 | opls_801 C801 12.0110 -0.269 A 3.50000E-01 2.76144E-01 20 | opls_807 H807 1.0080 0.000 A 2.50000E-01 1.25520E-01 21 | opls_804 H804 1.0080 0.000 A 2.50000E-01 1.25520E-01 22 | opls_805 H805 1.0080 0.000 A 2.50000E-01 1.25520E-01 23 | opls_806 H806 1.0080 0.192 A 2.50000E-01 1.25520E-01 24 | opls_802 Cl802 35.4500 0.001 A 3.40000E-01 1.25520E+00 25 | 26 | 27 | [ moleculetype ] 28 | ; name nrexcl 29 | MOL 3 30 | 31 | 32 | [ atoms ] 33 | ; nr type resnr residue atom cgnr charge mass 34 | 1 opls_800 1 MOL C00 1 -0.488 12.0110 35 | 2 opls_801 1 MOL C01 1 -0.269 12.0110 36 | 3 opls_802 1 MOL Cl0 1 0.001 35.4500 37 | 4 opls_803 1 MOL H03 1 0.124 1.0080 38 | 5 opls_803 1 MOL H04 1 0.124 1.0080 39 | 6 opls_803 1 MOL H05 1 0.124 1.0080 40 | 7 opls_806 1 MOL H06 1 0.192 1.0080 41 | 8 opls_806 1 MOL H07 1 0.192 1.0080 42 | 43 | 44 | [ bonds ] 45 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 46 | 2 1 1 0.1529 224262.400 47 | 3 2 1 0.1781 205016.000 48 | 4 1 1 0.1090 284512.000 49 | 5 1 1 0.1090 284512.000 50 | 6 1 1 0.1090 284512.000 51 | 7 2 1 0.1090 284512.000 52 | 8 2 1 0.1090 284512.000 53 | 54 | 55 | [ angles ] 56 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 57 | 1 2 3 1 109.800 577.392 58 | 2 1 4 1 110.700 313.800 59 | 2 1 5 1 110.700 313.800 60 | 2 1 6 1 110.700 313.800 61 | 1 2 7 1 110.700 313.800 62 | 1 2 8 1 110.700 313.800 63 | 4 1 5 1 107.800 276.144 64 | 5 1 6 1 107.800 276.144 65 | 3 2 7 1 107.600 426.768 66 | 3 2 8 1 107.600 426.768 67 | 4 1 6 1 107.800 276.144 68 | 7 2 8 1 107.800 276.144 69 | 70 | 71 | [ dihedrals ] 72 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 73 | 4 1 2 3 3 0.837 2.510 0.000 -3.347 -0.000 0.000 74 | 5 1 2 3 3 0.837 2.510 0.000 -3.347 -0.000 0.000 75 | 6 1 2 3 3 0.837 2.510 0.000 -3.347 -0.000 0.000 76 | 8 2 1 6 3 0.628 1.883 0.000 -2.510 -0.000 0.000 77 | 7 2 1 5 3 0.628 1.883 0.000 -2.510 -0.000 0.000 78 | 8 2 1 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 79 | 8 2 1 5 3 0.628 1.883 0.000 -2.510 -0.000 0.000 80 | 7 2 1 6 3 0.628 1.883 0.000 -2.510 -0.000 0.000 81 | 7 2 1 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 82 | 83 | 84 | -------------------------------------------------------------------------------- /Solvents/1,2-dibromoethane/1,2-dibromoethane.itp: -------------------------------------------------------------------------------- 1 | ; 1,2-dibromoethane 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_800 Br800 79.9040 0.235 A 3.47000E-01 1.96648E+00 18 | opls_801 C801 12.0110 -0.641 A 3.50000E-01 2.76144E-01 19 | opls_807 H807 1.0080 0.000 A 2.50000E-01 1.25520E-01 20 | opls_804 H804 1.0080 0.203 A 2.50000E-01 1.25520E-01 21 | opls_802 C802 12.0110 0.000 A 3.50000E-01 2.76144E-01 22 | opls_803 Br803 79.9040 0.000 A 3.47000E-01 1.96648E+00 23 | opls_805 H805 1.0080 0.000 A 2.50000E-01 1.25520E-01 24 | opls_806 H806 1.0080 0.000 A 2.50000E-01 1.25520E-01 25 | 26 | 27 | [ moleculetype ] 28 | ; name nrexcl 29 | MOL 3 30 | 31 | 32 | [ atoms ] 33 | ; nr type resnr residue atom cgnr charge mass 34 | 1 opls_800 1 MOL Br0 1 0.235 79.9040 35 | 2 opls_801 1 MOL C01 1 -0.641 12.0110 36 | 3 opls_801 1 MOL C02 1 -0.641 12.0110 37 | 4 opls_800 1 MOL Br3 1 0.235 79.9040 38 | 5 opls_804 1 MOL H04 1 0.203 1.0080 39 | 6 opls_804 1 MOL H05 1 0.203 1.0080 40 | 7 opls_804 1 MOL H06 1 0.203 1.0080 41 | 8 opls_804 1 MOL H07 1 0.203 1.0080 42 | 43 | 44 | [ bonds ] 45 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 46 | 2 1 1 0.1945 205016.000 47 | 3 2 1 0.1529 224262.400 48 | 4 3 1 0.1945 205016.000 49 | 5 2 1 0.1090 284512.000 50 | 6 2 1 0.1090 284512.000 51 | 7 3 1 0.1090 284512.000 52 | 8 3 1 0.1090 284512.000 53 | 54 | 55 | [ angles ] 56 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 57 | 1 2 3 1 110.000 577.392 58 | 2 3 4 1 110.000 577.392 59 | 1 2 5 1 107.600 426.768 60 | 1 2 6 1 107.600 426.768 61 | 2 3 7 1 110.700 313.800 62 | 2 3 8 1 110.700 313.800 63 | 4 3 8 1 107.600 426.768 64 | 5 2 6 1 107.800 276.144 65 | 7 3 8 1 107.800 276.144 66 | 3 2 5 1 110.700 313.800 67 | 3 2 6 1 110.700 313.800 68 | 4 3 7 1 107.600 426.768 69 | 70 | 71 | [ dihedrals ] 72 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 73 | 4 3 2 1 3 0.837 2.510 0.000 -3.347 -0.000 0.000 74 | 6 2 3 4 3 0.837 2.510 0.000 -3.347 -0.000 0.000 75 | 8 3 2 1 3 0.837 2.510 0.000 -3.347 -0.000 0.000 76 | 5 2 3 4 3 0.837 2.510 0.000 -3.347 -0.000 0.000 77 | 7 3 2 1 3 0.837 2.510 0.000 -3.347 -0.000 0.000 78 | 7 3 2 5 3 0.628 1.883 0.000 -2.510 -0.000 0.000 79 | 8 3 2 5 3 0.628 1.883 0.000 -2.510 -0.000 0.000 80 | 7 3 2 6 3 0.628 1.883 0.000 -2.510 -0.000 0.000 81 | 8 3 2 6 3 0.628 1.883 0.000 -2.510 -0.000 0.000 82 | 83 | 84 | -------------------------------------------------------------------------------- /Solvents/pentachloroethane/pentachloroethane.itp: -------------------------------------------------------------------------------- 1 | ; pentachloroethane 2 | ; 3 | ; Zhong, X.; Velez, C.; Acevedo, O. 4 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 5 | ; J. Chem. Theory Comput. 2021, 17, (in press). 6 | ; doi: 10.1021/acs.jctc.1c00047. 7 | ; 8 | ; GAML charges with OPLS-AA 9 | ; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/ 10 | ; Jorgensen Lab @ Yale University 11 | ; 12 | ; GROMACS 5.0.7 is recommended for the values given below 13 | 14 | 15 | [ atomtypes ] 16 | ; type name mass charge ptype sigma(nm) epsilon(kj/mol) 17 | opls_801 C801 12.0110 -0.027 A 3.50000E-01 2.76144E-01 18 | opls_803 C803 12.0110 0.33 A 3.50000E-01 2.76144E-01 19 | opls_805 Cl805 35.4500 0.000 A 3.40000E-01 1.25520E+00 20 | opls_806 Cl806 35.4500 0.000 A 3.40000E-01 1.25520E+00 21 | opls_807 H807 1.0080 0.165 A 2.50000E-01 1.25520E-01 22 | opls_804 Cl804 35.4500 -0.14 A 3.40000E-01 1.25520E+00 23 | opls_802 Cl802 35.4500 0.000 A 3.40000E-01 1.25520E+00 24 | opls_800 Cl800 35.4500 -0.024 A 3.40000E-01 1.25520E+00 25 | 26 | 27 | [ moleculetype ] 28 | ; name nrexcl 29 | MOL 3 30 | 31 | 32 | [ atoms ] 33 | ; nr type resnr residue atom cgnr charge mass 34 | 1 opls_800 1 MOL Cl0 1 -0.024 35.4500 35 | 2 opls_801 1 MOL C01 1 -0.027 12.0110 36 | 3 opls_800 1 MOL Cl1 1 -0.024 35.4500 37 | 4 opls_803 1 MOL C03 1 0.33 12.0110 38 | 5 opls_804 1 MOL Cl2 1 -0.14 35.4500 39 | 6 opls_804 1 MOL Cl3 1 -0.14 35.4500 40 | 7 opls_804 1 MOL Cl4 1 -0.14 35.4500 41 | 8 opls_807 1 MOL H07 1 0.165 1.0080 42 | 43 | 44 | [ bonds ] 45 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 46 | 2 1 1 0.1781 205016.000 47 | 3 2 1 0.1781 205016.000 48 | 4 2 1 0.1529 224262.400 49 | 5 4 1 0.1781 205016.000 50 | 6 4 1 0.1781 205016.000 51 | 7 4 1 0.1781 205016.000 52 | 8 2 1 0.1090 284512.000 53 | 54 | 55 | [ angles ] 56 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 57 | 1 2 3 1 111.700 652.704 58 | 1 2 4 1 109.800 577.392 59 | 2 4 5 1 109.800 577.392 60 | 2 4 6 1 109.800 577.392 61 | 2 4 7 1 109.800 577.392 62 | 1 2 8 1 107.600 426.768 63 | 4 2 8 1 110.700 313.800 64 | 5 4 6 1 111.700 652.704 65 | 3 2 4 1 109.800 577.392 66 | 5 4 7 1 111.700 652.704 67 | 3 2 8 1 107.600 426.768 68 | 6 4 7 1 111.700 652.704 69 | 70 | 71 | [ dihedrals ] 72 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 73 | 5 4 2 1 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 74 | 6 4 2 1 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 75 | 7 4 2 3 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 76 | 5 4 2 3 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 77 | 7 4 2 1 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 78 | 6 4 2 3 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 79 | 8 2 4 5 3 0.837 2.510 0.000 -3.347 -0.000 0.000 80 | 8 2 4 6 3 0.837 2.510 0.000 -3.347 -0.000 0.000 81 | 8 2 4 7 3 0.837 2.510 0.000 -3.347 -0.000 0.000 82 | 83 | 84 | --------------------------------------------------------------------------------