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Merge pull request #60 from open-forcefield-group/smirff_energy_check
Cross-check SMIRFF energies vs parm@frosst on full AlkEthOH set (finished, tests added)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| #!/bin/env python | ||
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| from smarty.forcefield_utils import * | ||
| import os | ||
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| # Cross-check energies of molecules from AlkEthOH set using SMIRFF xml file | ||
| # versus energies from AMBER .prmtop and .crd files (parm@frosst params) | ||
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| datapath = './AlkEthOH_inputfiles/AlkEthOH_rings_filt1' | ||
| #molname = 'AlkEthOH_r0' #That fails, but it's complicated. Try cyclobutane | ||
| molname = 'AlkEthOH_r51' | ||
| mol_filename = os.path.join( datapath, molname+'.mol2') | ||
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| # Check if we have this data file; if not we have to extract the archive | ||
| if not os.path.isfile( mol_filename): | ||
| print "Extracting archived molecule files." | ||
| tarfile = 'AlkEthOH_inputfiles.tar.gz' | ||
| os.system('tar -xf AlkEthOH_inputfiles.tar.gz') | ||
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| # Load OEMol | ||
| mol = oechem.OEGraphMol() | ||
| ifs = oechem.oemolistream(mol_filename) | ||
| flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield | ||
| ifs.SetFlavor( oechem.OEFormat_MOL2, flavor) | ||
| oechem.OEReadMolecule(ifs, mol ) | ||
| oechem.OETriposAtomNames(mol) | ||
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| # Load forcefield | ||
| forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH_parmAtFrosst.ffxml')) | ||
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| # Compare energies | ||
| prmtop = os.path.join( datapath, molname+'.top') | ||
| crd = os.path.join( datapath, molname+'.crd') | ||
| results = compare_molecule_energies( prmtop, crd, forcefield, mol) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| AlkEthOH_c100 | ||
| 26 | ||
| -0.9553000 0.4818000 -0.2077000 -0.3490000 1.5118000 -3.9233000 | ||
| 2.2817000 2.6277000 -0.7960000 1.2497000 4.6992000 -1.7325000 | ||
| -1.2082000 0.6003000 -1.7062000 -0.0897000 1.3641000 -2.4285000 | ||
| 1.3968000 3.1877000 -1.9119000 -2.4504000 1.2717000 -1.9070000 | ||
| 2.0195000 2.9930000 -3.1820000 0.0656000 2.6662000 -1.8674000 | ||
| -0.8584000 1.4672000 0.2604000 -0.0508000 -0.0987000 -0.0023000 | ||
| -1.8018000 -0.0117000 0.2823000 -1.2912000 2.0347000 -4.1123000 | ||
| 0.4621000 2.0550000 -4.4201000 -0.3970000 0.5255000 -4.3979000 | ||
| 2.4059000 1.5440000 -0.8979000 3.2673000 3.1044000 -0.7929000 | ||
| 1.8318000 2.7934000 0.1888000 0.6177000 5.1189000 -2.5244000 | ||
| 2.2188000 5.2065000 -1.7918000 0.7741000 4.9438000 -0.7766000 | ||
| -1.2996000 -0.4020000 -2.1404000 0.8600000 0.8372000 -2.2840000 | ||
| -3.1291000 0.7293000 -1.4768000 2.8732000 3.4574000 -3.1770000 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| @<TRIPOS>MOLECULE | ||
| AlkEthOH_c100 | ||
| 26 25 1 0 0 | ||
| SMALL | ||
| USER_CHARGES | ||
|
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| @<TRIPOS>ATOM | ||
| 1 C1 -0.9553 0.4818 -0.2077 CT 1 <0> -0.12819 | ||
| 2 C2 -0.3490 1.5118 -3.9233 CT 1 <0> -0.11278 | ||
| 3 C3 2.2817 2.6277 -0.7960 CT 1 <0> -0.13028 | ||
| 4 C4 1.2497 4.6992 -1.7325 CT 1 <0> -0.13028 | ||
| 5 C5 -1.2082 0.6003 -1.7062 CT 1 <0> 0.13828 | ||
| 6 C6 -0.0897 1.3641 -2.4285 CT 1 <0> 0.17039 | ||
| 7 C7 1.3968 3.1877 -1.9119 CT 1 <0> 0.34809 | ||
| 8 O1 -2.4504 1.2717 -1.9070 OH 1 <0> -0.58269 | ||
| 9 O2 2.0195 2.9930 -3.1820 OH 1 <0> -0.62548 | ||
| 10 O3 0.0656 2.6662 -1.8674 OS 1 <0> -0.40486 | ||
| 11 H1 -0.8584 1.4672 0.2604 HC 1 <0> 0.04431 | ||
| 12 H2 -0.0508 -0.0987 -0.0023 HC 1 <0> 0.04431 | ||
| 13 H3 -1.8018 -0.0117 0.2823 HC 1 <0> 0.04431 | ||
| 14 H4 -1.2912 2.0347 -4.1123 HC 1 <0> 0.04980 | ||
| 15 H5 0.4621 2.0550 -4.4201 HC 1 <0> 0.04980 | ||
| 16 H6 -0.3970 0.5255 -4.3979 HC 1 <0> 0.04980 | ||
| 17 H7 2.4059 1.5440 -0.8979 HC 1 <0> 0.05049 | ||
| 18 H8 3.2673 3.1044 -0.7929 HC 1 <0> 0.05049 | ||
| 19 H9 1.8318 2.7934 0.1888 HC 1 <0> 0.05049 | ||
| 20 H10 0.6177 5.1189 -2.5244 HC 1 <0> 0.05049 | ||
| 21 H11 2.2188 5.2065 -1.7918 HC 1 <0> 0.05049 | ||
| 22 H12 0.7741 4.9438 -0.7766 HC 1 <0> 0.05049 | ||
| 23 H13 -1.2996 -0.4020 -2.1404 H1 1 <0> 0.02625 | ||
| 24 H14 0.8600 0.8372 -2.2840 H1 1 <0> 0.04199 | ||
| 25 H15 -3.1291 0.7293 -1.4768 HO 1 <0> 0.39414 | ||
| 26 H16 2.8732 3.4574 -3.1770 HO 1 <0> 0.41015 | ||
| @<TRIPOS>BOND | ||
| 1 1 5 1 | ||
| 2 2 6 1 | ||
| 3 3 7 1 | ||
| 4 4 7 1 | ||
| 5 5 6 1 | ||
| 6 5 8 1 | ||
| 7 6 10 1 | ||
| 8 7 9 1 | ||
| 9 7 10 1 | ||
| 10 1 11 1 | ||
| 11 1 12 1 | ||
| 12 1 13 1 | ||
| 13 2 14 1 | ||
| 14 2 15 1 | ||
| 15 2 16 1 | ||
| 16 3 17 1 | ||
| 17 3 18 1 | ||
| 18 3 19 1 | ||
| 19 4 20 1 | ||
| 20 4 21 1 | ||
| 21 4 22 1 | ||
| 22 5 23 1 | ||
| 23 6 24 1 | ||
| 24 8 25 1 | ||
| 25 9 26 1 | ||
| @<TRIPOS>SUBSTRUCTURE | ||
| 1 <0> 1 GROUP 0 A **** |
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