mirror of
https://github.com/openmm/openmm
synced 2026-06-03 06:39:48 +09:00
939e0af545
* Add basic version of TinkerFiles * Refactor TinkerFiles * Update docstring, type hints, and fix bug when setting box vectors * Small fixes * Add unit tests for the TinkerFiles class * Fixes and updates to TinkerFiles * Add simuteTinker example * Update Modeller to work with AMOEBA force fields * Small fixes * Relax type hinting * Fix indices in modeller * Fix modeller indices * Fix type hints and usage of Quantity * Remove numpy protector * Add reader of .seq files * Add topology parsing of some protein residues, waters, ions, and generic molecules. * Miscellaneous improvements * Update amino acids and nucleotides list * Various fixes to XML writing, and separate XML writing into a new class * Comments/warnings * Add nucleic topological definitions * Improved handling of peptide residues * Fix for CYX (disulfide bonds) * Refactor the topology creation methods * General improvements, and add support for nucleic-like residues * No need to handle MP, DP, TP * Minor improvements * General refactoring, add automatic determination of topology * Add TinkerAtomType dataclass, and remove references to biotypes as they are not needed * Re-add missing parsing of forces and scalars * Updates to createSystem() * Add AMOEBA forces * Add angle-related forces to createSystem * Add placeholders for missing forces * Beginning of support for AmoebaMultipoleForce * Finished support for AmoebaMultipoleForce * Support for AmoebaVdwForce * TinkerFiles supports vdw * Misc updates, and add AmoebaTorsionTorsion, AmoebaWcaDispersion, and AmoebaGeneralizedKirkwood * Remove XML writer * Fixes * Fix wrong indentation in _findBitorsions * Remove pdb debugging * Documentation and fixes * Remove files * Revert checks in AmoebaVdwForceBuilder and ## @private markers * Remove duplicated static methods _getChiralAtomIndex * Fix GK force * Fix WcaDispersion force * Fix WcaDisp * Fixes and updates * Cleanup and removing duplicated code * Bug fixes * A few more unit conversions * Minor cleanup * Misc fixes and updates * Fix Add AmoebaStretchBendForce * Simplify force builders * Update ForceField * Fix AmoebaPiTorsionForce * Only add AmoebaWcaDispersionForce if using implicitSolvent * Simplify amoebaforces * Stretch torsion and angle torsion * Misc. fixes * Improve tests * Fix cap group identification * Add/improve tests * Remove whitespaces from residue names * Improve tests * Consistent use of atomClasses list * Fix match condition in AmoebaOutOfPlaneBendForceBuilder * Fix AmoebaStretchBendForce * Final fix for AmoebaStretchBendForce * Fix AmoebaAngleForce * Small fixes and improvements * Update assertion tolerances * Simplify torsion-torsion force creation * Small fixes in the tests * Review comments, type hints, docs for tinkerfiles.py * Only use standard PDB for AA * Type hint and docs for amoebaforces * Reduce tolerances for failing tests * Fixed error with ZOnly axis type when x particle is not specified --------- Co-authored-by: peastman <peastman@stanford.edu>
426 lines
22 KiB
Promela
426 lines
22 KiB
Promela
vdw-lambda 1
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ele-lambda 0.1
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ligand -1 13
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c-axis 35.7
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b-axis 35.7
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a-axis 35.7
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OPENMP-THREADS 1
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polarization MUTUAL
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pme-order 5
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pme-grid 64 64 64
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vdw-annihilate
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vdw-correction
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neighbor-list
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barostat montecarlo
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polar-predict
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polar-eps 1e-05
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ewald-cutoff 7
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vdw-cutoff 12
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ewald
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thermostat BUSSI
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integrator RESPA
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archive
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parameters amoebabio18.prm
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digits 8
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RESP-WEIGHT 1
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#############################
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## ##
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## Literature References ##
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## ##
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#############################
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Wu, J.C.; Chattree, G.; Ren, P.Y.; Automation of AMOEBA polarizable force field
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parameterization for small molecules. Theor Chem Acc.
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atom 405 405 O "phenol " 8 15.999 2
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atom 404 404 C "phenol " 6 12.011 3
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atom 401 401 C "phenol " 6 12.011 3
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atom 403 403 C "phenol " 6 12.011 3
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atom 402 402 C "phenol " 6 12.011 3
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atom 408 408 H "phenol " 1 1.008 1
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atom 406 406 H "phenol " 1 1.008 1
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atom 407 407 H "phenol " 1 1.008 1
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atom 409 409 H "phenol " 1 1.008 1
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [13]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [13]]] with tinker type descriptions [[('H', '"Phenol HO"')]]
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# [409] = [[13]]
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vdw 409 2.6550 0.0135 0.910
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [2]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [2]]] with tinker type descriptions [[('C', '"Phenol C1-OH"')]]
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# [404] = [[2]]
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vdw 404 3.8000 0.0910
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [7]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [7]]] with tinker type descriptions [[('C', '"Phenol C2"')]]
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# [401] = [[3, 4]]
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vdw 401 3.8000 0.0910
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [6]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [6]]] with tinker type descriptions [[('C', '"Phenol C3"')]]
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# [403] = [[5, 6]]
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vdw 403 3.8000 0.0910
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [5]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [5]]] with tinker type descriptions [[('C', '"Phenol C4"')]]
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# [402] = [[7]]
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vdw 402 3.8000 0.0910
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [8]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [8]]] with tinker type descriptions [[('H', '"Phenol H2"')]]
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# [408] = [[8, 9]]
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vdw 408 2.9800 0.0260 0.920
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [9]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [9]]] with tinker type descriptions [[('H', '"Phenol H3"')]]
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# [406] = [[10, 11]]
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vdw 406 2.9800 0.0260 0.920
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [10]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [10]]] with tinker type descriptions [[('H', '"Phenol H4"')]]
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# [407] = [[12]]
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vdw 407 2.9800 0.0260 0.920
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# matching SMARTS from molecule ('[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', (1,)) from external database
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# [405] = [[1]]
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vdw 405 3.356 0.1188
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# updated valence parameter database match, comments=car, O on Phenol SMARTS match = [c] [OH]([cccccc])
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# [404, 405] = [[2], [1]]
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bond 404 405 307.149735 1.37
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# updated valence parameter database match, comments=HO, H on Oxygen O on Phenol SMARTS match = [H][OH1] [OH]([cccccc])
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# [409, 405] = [[13], [1]]
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bond 409 405 511.459981 0.97
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# updated valence parameter database match, comments=car, car, SMARTS match = [c] [c]
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# [401, 404] = [[3, 4], [2]]
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bond 401 404 379.094345 1.4
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# updated valence parameter database match, comments=car, car, SMARTS match = [c] [c]
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# [403, 401] = [[5, 6], [3, 4]]
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bond 403 401 379.094345 1.39
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, SMARTS match = [H][c] [c]
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# [408, 401] = [[8, 9], [3, 4]]
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bond 408 401 368.093365 1.09
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# updated valence parameter database match, comments=car, car, SMARTS match = [c] [c]
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# [402, 403] = [[7], [5, 6]]
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bond 402 403 379.094345 1.39
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, SMARTS match = [H][c] [c]
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# [406, 403] = [[10, 11], [5, 6]]
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bond 406 403 368.093365 1.09
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, SMARTS match = [H][c] [c]
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# [407, 402] = [[12], [7]]
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bond 407 402 368.093365 1.09
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# updated valence parameter database match, comments=car, car, O on Phenol SMARTS match = [c] [c] [OH]([cccccc])
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# [401, 404, 405] = [[3, 4], [2], [1]]
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angle 401 404 405 88.716479 119.87
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# updated valence parameter database match, comments=HO, H on Oxygen O on Phenol car, SMARTS match = [H][OH1] [OH]([cccccc]) [c]
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# [409, 405, 404] = [[13], [1], [2]]
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angle 409 405 404 49.6767 106.78680000000001
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# updated valence parameter database match, comments=car, car, car, SMARTS match = [c] [c] [c]
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# [403, 401, 404] = [[5, 6], [3, 4], [2]]
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angle 403 401 404 74.630713 119.62
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, car, SMARTS match = [H][c] [c] [c]
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# [408, 401, 404] = [[8, 9], [3, 4], [2]]
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angle 408 401 404 36.770174 119.46
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# updated valence parameter database match, comments=car, car, car, SMARTS match = [c] [c] [c]
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# [401, 404, 401] = [[3, 4], [2], [3, 4]]
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angle 401 404 401 74.630713 120.27
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# updated valence parameter database match, comments=car, car, car, SMARTS match = [c] [c] [c]
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# [402, 403, 401] = [[7], [5, 6], [3, 4]]
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angle 402 403 401 74.630713 120.53
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, car, SMARTS match = [H][c] [c] [c]
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# [406, 403, 401] = [[10, 11], [5, 6], [3, 4]]
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angle 406 403 401 36.770174 119.32
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, car, SMARTS match = [H][c] [c] [c]
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# [408, 401, 403] = [[8, 9], [3, 4], [5, 6]]
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angle 408 401 403 36.770174 120.92
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# updated valence parameter database match, comments=car, car, car, SMARTS match = [c] [c] [c]
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# [403, 402, 403] = [[5, 6], [7], [5, 6]]
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angle 403 402 403 74.630713 119.43
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, car, SMARTS match = [H][c] [c] [c]
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# [407, 402, 403] = [[12], [7], [5, 6]]
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angle 407 402 403 36.770174 120.29
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, car, SMARTS match = [H][c] [c] [c]
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# [406, 403, 402] = [[10, 11], [5, 6], [7]]
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angle 406 403 402 36.770174 120.14
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# updated valence parameter database match, comments=car, car, O on Phenol SMARTS match = [c] [c] [OH]([cccccc])
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# [401, 404, 405] = [[3, 4], [2], [1]]
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strbnd 401 404 405 20.4528 20.4528
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# updated valence parameter database match, comments=HO, H on Oxygen O on Phenol car, SMARTS match = [H][OH1] [OH]([cccccc]) [c]
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# [409, 405, 404] = [[13], [1], [2]]
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strbnd 409 405 404 17.3182 -17.3182
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# updated valence parameter database match, comments=car, car, car, SMARTS match = [c] [c] [c]
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# [403, 401, 404] = [[5, 6], [3, 4], [2]]
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strbnd 403 401 404 20.4528 20.4528
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, car, SMARTS match = [H][c] [c] [c]
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# [408, 401, 404] = [[8, 9], [3, 4], [2]]
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strbnd 408 401 404 20.4528 20.4528
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# updated valence parameter database match, comments=car, car, car, SMARTS match = [c] [c] [c]
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# [401, 404, 401] = [[3, 4], [2], [3, 4]]
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strbnd 401 404 401 20.4528 20.4528
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# updated valence parameter database match, comments=car, car, car, SMARTS match = [c] [c] [c]
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# [402, 403, 401] = [[7], [5, 6], [3, 4]]
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strbnd 402 403 401 20.4528 20.4528
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, car, SMARTS match = [H][c] [c] [c]
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# [406, 403, 401] = [[10, 11], [5, 6], [3, 4]]
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strbnd 406 403 401 20.4528 20.4528
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, car, SMARTS match = [H][c] [c] [c]
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# [408, 401, 403] = [[8, 9], [3, 4], [5, 6]]
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strbnd 408 401 403 20.4528 20.4528
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# updated valence parameter database match, comments=car, car, car, SMARTS match = [c] [c] [c]
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# [403, 402, 403] = [[5, 6], [7], [5, 6]]
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strbnd 403 402 403 20.4528 20.4528
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, car, SMARTS match = [H][c] [c] [c]
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# [407, 402, 403] = [[12], [7], [5, 6]]
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strbnd 407 402 403 20.4528 20.4528
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, car, SMARTS match = [H][c] [c] [c]
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# [406, 403, 402] = [[10, 11], [5, 6], [7]]
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strbnd 406 403 402 20.4528 20.4528
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# updated valence parameter database match, comments=car, O on Phenol SMARTS match = [c] [OH]([cccccc])
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# [405, 404] = [[1], [2]]
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opbend 405 404 0 0 28.2725
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# updated valence parameter database match, comments=car, car, SMARTS match = [c] [c]
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# [401, 404] = [[3, 4], [2]]
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opbend 401 404 0 0 84.8861
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# updated valence parameter database match, comments=car, car, SMARTS match = [c] [c]
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# [404, 401] = [[2], [3, 4]]
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opbend 404 401 0 0 84.8861
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# updated valence parameter database match, comments=car, car, SMARTS match = [c] [c]
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# [403, 401] = [[5, 6], [3, 4]]
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opbend 403 401 0 0 84.8861
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# updated valence parameter database match, comments=car, car, SMARTS match = [c] [c]
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# [401, 403] = [[3, 4], [5, 6]]
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opbend 401 403 0 0 84.8861
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, SMARTS match = [H][c] [c]
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# [408, 401] = [[8, 9], [3, 4]]
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opbend 408 401 0 0 72.8135
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# updated valence parameter database match, comments=car, car, SMARTS match = [c] [c]
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# [402, 403] = [[7], [5, 6]]
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opbend 402 403 0 0 84.8861
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# updated valence parameter database match, comments=car, car, SMARTS match = [c] [c]
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# [403, 402] = [[5, 6], [7]]
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opbend 403 402 0 0 84.8861
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, SMARTS match = [H][c] [c]
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# [406, 403] = [[10, 11], [5, 6]]
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opbend 406 403 0 0 72.8135
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# updated valence parameter database match, comments=HC, H on aromatic carbon car, SMARTS match = [H][c] [c]
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# [407, 402] = [[12], [7]]
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opbend 407 402 0 0 72.8135
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [13, 1, 2, 7]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [13, 1, 2, 7]]] with tinker type descriptions [[('H', '"Phenol HO"'), ('O', '"Phenol OH"'), ('C', '"Phenol C1-OH"'), ('C', '"Phenol C2"')]]
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# [401, 404, 405, 409] = [[3, 4], [2], [1], [13]]
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torsion 401 404 405 409 0.000 0.0 1 2.081 180.0 2 0.000 0.0 3
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [6, 7, 2, 1]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [6, 7, 2, 1]]] with tinker type descriptions [[('C', '"Phenol C3"'), ('C', '"Phenol C2"'), ('C', '"Phenol C1-OH"'), ('O', '"Phenol OH"')]]
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# [403, 401, 404, 405] = [[5, 6], [3, 4], [2], [1]]
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torsion 403 401 404 405 0.000 0.0 1 6.182499999999999 180.0 2 0.000 0.0 3
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [8, 7, 2, 1]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [8, 7, 2, 1]]] with tinker type descriptions [[('H', '"Phenol H2"'), ('C', '"Phenol C2"'), ('C', '"Phenol C1-OH"'), ('O', '"Phenol OH"')]]
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# [408, 401, 404, 405] = [[8, 9], [3, 4], [2], [1]]
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torsion 408 401 404 405 0.000 0.0 1 6.182499999999999 180.0 2 0.000 0.0 3
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [5, 6, 7, 2]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [5, 6, 7, 2]]] with tinker type descriptions [[('C', '"Phenol C4"'), ('C', '"Phenol C3"'), ('C', '"Phenol C2"'), ('C', '"Phenol C1-OH"')]]
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# [402, 403, 401, 404] = [[7], [5, 6], [3, 4], [2]]
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torsion 402 403 401 404 -0.670 0.0 1 6.287333333333333 180.0 2 0.000 0.0 3
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [4, 3, 2, 7]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [4, 3, 2, 7]]] with tinker type descriptions [[('C', '"Phenol C3"'), ('C', '"Phenol C2"'), ('C', '"Phenol C1-OH"'), ('C', '"Phenol C2"')]]
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# [403, 401, 404, 401] = [[5, 6], [3, 4], [2], [3, 4]]
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torsion 403 401 404 401 -0.670 0.0 1 5.7165 180.0 2 0.000 0.0 3
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [4, 5, 6, 7]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [4, 5, 6, 7]]] with tinker type descriptions [[('C', '"Phenol C3"'), ('C', '"Phenol C4"'), ('C', '"Phenol C3"'), ('C', '"Phenol C2"')]]
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# [403, 402, 403, 401] = [[5, 6], [7], [5, 6], [3, 4]]
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torsion 403 402 403 401 -0.670 0.0 1 6.287333333333333 180.0 2 0.000 0.0 3
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [9, 6, 7, 2]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [9, 6, 7, 2]]] with tinker type descriptions [[('H', '"Phenol H3"'), ('C', '"Phenol C3"'), ('C', '"Phenol C2"'), ('C', '"Phenol C1-OH"')]]
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# [406, 403, 401, 404] = [[10, 11], [5, 6], [3, 4], [2]]
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torsion 406 403 401 404 0.550 0.0 1 6.817333333333333 180.0 2 -0.550 0.0 3
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [12, 3, 2, 7]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [12, 3, 2, 7]]] with tinker type descriptions [[('H', '"Phenol H2"'), ('C', '"Phenol C2"'), ('C', '"Phenol C1-OH"'), ('C', '"Phenol C2"')]]
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# [408, 401, 404, 401] = [[8, 9], [3, 4], [2], [3, 4]]
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torsion 408 401 404 401 0.550 0.0 1 6.246499999999999 180.0 2 -0.550 0.0 3
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [10, 5, 6, 7]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [10, 5, 6, 7]]] with tinker type descriptions [[('H', '"Phenol H4"'), ('C', '"Phenol C4"'), ('C', '"Phenol C3"'), ('C', '"Phenol C2"')]]
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# [407, 402, 403, 401] = [[12], [7], [5, 6], [3, 4]]
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torsion 407 402 403 401 0.550 0.0 1 6.817333333333333 180.0 2 -0.550 0.0 3
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [11, 4, 5, 6]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [11, 4, 5, 6]]] with tinker type descriptions [[('H', '"Phenol H3"'), ('C', '"Phenol C3"'), ('C', '"Phenol C4"'), ('C', '"Phenol C3"')]]
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# [406, 403, 402, 403] = [[10, 11], [5, 6], [7], [5, 6]]
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torsion 406 403 402 403 0.550 0.0 1 11.384 180.0 2 -0.550 0.0 3
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [8, 7, 6, 5]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [8, 7, 6, 5]]] with tinker type descriptions [[('H', '"Phenol H2"'), ('C', '"Phenol C2"'), ('C', '"Phenol C3"'), ('C', '"Phenol C4"')]]
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# [408, 401, 403, 402] = [[8, 9], [3, 4], [5, 6], [7]]
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torsion 408 401 403 402 0.550 0.0 1 11.384 180.0 2 -0.550 0.0 3
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [9, 6, 7, 8]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [9, 6, 7, 8]]] with tinker type descriptions [[('H', '"Phenol H3"'), ('C', '"Phenol C3"'), ('C', '"Phenol C2"'), ('H', '"Phenol H2"')]]
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# [406, 403, 401, 408] = [[10, 11], [5, 6], [3, 4], [8, 9]]
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torsion 406 403 401 408 0.000 0.0 1 6.355333333333333 180.0 2 0.000 0.0 3
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# matching SMARTS from molecule [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#1])-[#1])-[#1])-[#1])-[#1])-[#1]', [10, 5, 6, 9]]] to SMARTS from parameter file [['[#8](-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[H])-[H])-[H])-[H])-[H])-[H]', [10, 5, 6, 9]]] with tinker type descriptions [[('H', '"Phenol H4"'), ('C', '"Phenol C4"'), ('C', '"Phenol C3"'), ('H', '"Phenol H3"')]]
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# [407, 402, 403, 406] = [[12], [7], [5, 6], [10, 11]]
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torsion 407 402 403 406 0.000 0.0 1 6.355333333333333 180.0 2 0.000 0.0 3
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#SOLUTE-SMARTS 409 [#1][O;D2][#6]
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SOLUTE 409 2.6533 3.392 2.9044
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#SOLUTE-SMARTS 408 [#1][#6;D3]
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SOLUTE 408 2.574 2.758 2.9054
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#SOLUTE-SMARTS 406 [#1][#6;D3]
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SOLUTE 406 2.574 2.758 2.9054
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#SOLUTE-SMARTS 407 [#1][#6;D3]
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SOLUTE 407 2.574 2.758 2.9054
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#SOLUTE-SMARTS 401 c([cH0])
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SOLUTE 401 3.8585 3.766 3.8448
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#SOLUTE-SMARTS 404 [cH0]
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SOLUTE 404 3.6909 3.766 4.4258
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#SOLUTE-SMARTS 403 c(c([cH0]))
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SOLUTE 403 3.8286 3.893 4.5084
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#SOLUTE-SMARTS 402 c(c(c([cH0])))
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SOLUTE 402 3.8286 3.893 4.5084
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#SOLUTE-SMARTS 405 [O;D2][#6]
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SOLUTE 405 3.1684 3.134 3.0999
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# [405] = [[1]]
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polarize 405 0.8122 0.3900 409
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# updated valence parameter database match, comments=C on conjugated systems SMARTS match = [c]
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# [404] = [[2]]
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polarize 404 2.0645 0.3900 401
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# updated valence parameter database match, comments=C on conjugated systems SMARTS match = [c]
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# [401] = [[3, 4]]
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polarize 401 2.0645 0.3900 404 403 408
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# updated valence parameter database match, comments=C on conjugated systems SMARTS match = [c]
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# [403] = [[5, 6]]
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polarize 403 2.0645 0.3900 401 402 406
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# updated valence parameter database match, comments=C on conjugated systems SMARTS match = [c]
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# [402] = [[7]]
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polarize 402 2.0645 0.3900 403 407
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# updated valence parameter database match, comments=H on C=C system SMARTS match = [H][c]
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# [408] = [[8, 9]]
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polarize 408 0.4318 0.3900 401
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# updated valence parameter database match, comments=H on C=C system SMARTS match = [H][c]
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# [406] = [[10, 11]]
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polarize 406 0.4318 0.3900 403
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# updated valence parameter database match, comments=H on C=C system SMARTS match = [H][c]
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# [407] = [[12]]
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polarize 407 0.4318 0.3900 402
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# updated valence parameter database match, comments=H on HI SMARTS match = [H][O]
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# [409] = [[13]]
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polarize 409 0.4573 0.3900 405
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#
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# Multipoles from Electrostatic Potential Fitting
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#
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# [405] = [[1]]
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multipole 405 409 404 -0.46429
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0.16235 0.00000 0.18717
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-0.00450
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0.00000 -0.46498
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-0.06802 0.00000 0.46948
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# [404] = [[2]]
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multipole 404 -401 -401 0.33494
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0.00000 0.00000 -0.07119
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-0.20929
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0.00000 -0.32070
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0.00000 0.00000 0.52999
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# [401] = [[3, 4]]
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multipole 401 408 403 -0.12421
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0.10145 0.00000 0.17813
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0.25046
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0.00000 -0.16706
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0.01593 0.00000 -0.08340
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# [403] = [[5, 6]]
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multipole 403 406 402 0.08296
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0.00308 0.00000 -0.12200
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-0.21100
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0.00000 -0.39448
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0.04742 0.00000 0.60548
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# [402] = [[7]]
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multipole 402 -403 -403 -0.05316
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0.00000 0.00000 -0.11286
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0.23168
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0.00000 -0.22811
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0.00000 0.00000 -0.00357
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# [408] = [[8, 9]]
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multipole 408 401 403 0.00902
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0.02376 0.00000 -0.17062
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0.03893
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0.00000 0.01177
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-0.01143 0.00000 -0.05070
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# [406] = [[10, 11]]
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multipole 406 403 402 0.00755
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0.01255 0.00000 -0.15814
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0.12525
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0.00000 -0.02015
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0.00744 0.00000 -0.10510
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# [407] = [[12]]
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multipole 407 402 0.00466
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0.00000 0.00000 -0.18447
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0.03507
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0.00000 0.03507
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0.00000 0.00000 -0.07014
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# [409] = [[13]]
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multipole 409 405 404 0.22721
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0.02996 0.00000 -0.02605
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0.12347
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0.00000 -0.13670
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-0.08050 0.00000 0.01323
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