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Merge pull request #31 from martimunicoy/OPLS_addition
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Opls addition
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martimunicoy committed Aug 28, 2020
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16 changes: 15 additions & 1 deletion docs/releasehistory.rst
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Expand Up @@ -7,10 +7,24 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
* ``minor`` increments add features but do not break API compatibility
* ``micro`` increments represent bugfix releases or improvements in documentation


0.3.0 - Current development
-------------------------

This is still a preliminary version of the Open Force Field to PELE package.
This is a minor release that includes a refactoring of the classes and methods that involve the rotamer library builder. Besides, now it is possible to combine parameters from OPLS2005 and OFF. This release also contains a new method to define a molecule through a SMILES tag. It is still a preliminary version of the Open Force Field to PELE package which is under development.

New features
""""""""""""
- `PR #28 <https://github.com/martimunicoy/offpele/pull/28>`_: Adds a new method to define a `Molecule` object through a SMILES tag. This molecule can be written as a PDB file later for PELE.
- `PR #31 <https://github.com/martimunicoy/offpele/pull/31>`_: Adds the possibility to combine nonbonding and solvent parameters from OPLS2005 with bonding parameters from OFF.

Bugfixes
""""""""
- `PR #22 <https://github.com/martimunicoy/offpele/pull/22>`_: Fixes many bugs. For example, the default output name of the solvent parameters template is changed to `ligandParams.txt`, which is the name that PELE expects.

Tests added
"""""""""""
- `PR #31 <https://github.com/martimunicoy/offpele/pull/31>`_: Adds tests to validate some functions of the new SchrodingerToolkitWrapper.


0.2.1
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64 changes: 64 additions & 0 deletions offpele/data/parameters/f14_sgbnp.param
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#-------------------------------------------------------------------------------------------
# symbl sigma epsilon rxnf_r cav_r gamma alpha # comments
#-------------------------------------------------------------------------------------------
1 CT 1.750 0.066 1.975 1.750 0.005000000 -0.741685710 # alkanes C
1 CT5 1.750 0.066 1.838 1.625 0.005000000 -0.741685710 # alkanes C
1 CT6 1.750 0.066 2.495 1.750 0.005000000 -0.741685710 # alkanes C
1 CM 1.775 0.076 2.002 1.775 0.023028004 -0.852763146 # alkene C
1 CZ 1.825 0.150 2.058 1.825 0.025318638 -1.264311570 # alkyne C
1 CZN 1.625 0.066 1.810 1.600 0.025318638 -1.264311570 # nitrile C
1 CA 1.775 0.070 2.002 1.775 0.001000000 -0.843144165 # aromatic C
1 CA2 1.775 0.070 2.500 1.775 0.001000000 -0.843144165 # aromatic C
1 CA8 1.875 0.105 2.112 1.875 0.001000000 -0.126889456 # guanidine or guanidium
1 C 1.875 0.105 2.112 1.875 0.001000000 -0.126889456 # carbonyl C
1 CO2 1.875 0.105 2.112 1.875 0.001000000 -0.126889456 # carboxylate C
1 CN 1.875 0.105 1.925 1.700 0.001000000 -0.126889456 # carbonyl C of amides
1 C* 1.875 0.105 2.112 1.875 0.001000000 -0.126889456 # default C
2 O 1.480 0.210 1.678 1.480 0.001000000 -0.126889456 # carbonyl O
2 O2 1.480 0.210 1.700 1.500 0.001000000 -0.126889456 # carboxylate O
2 OC3 1.480 0.210 1.975 1.750 0.001000000 -0.126889456 # carboxylic acid, C=O
2 OCN1 1.480 0.210 1.810 1.600 0.001000000 -1.480495490 # carbonyl O (primary amide)
2 OCN 1.480 0.210 1.525 1.425 0.001000000 -1.480495490 # carbonyl O (general amide)
2 OH2 1.560 0.170 1.838 1.625 0.021068034 -0.322181743 # alcohols, phenols
2 OH 1.560 0.170 1.766 1.560 0.021068034 -0.322181743 # alcohols, phenols
2 OS 1.450 0.140 1.590 1.400 0.020110767 -0.896042159 # ethers, esters
2 OS2 1.450 0.140 1.766 1.560 0.020110767 -0.896042159 # ethers, esters
2 ON 1.480 0.170 1.865 1.650 0.020881802 -0.347800883 # nitro R-NO2
2 OZ 1.350 0.280 1.535 1.350 0.001000000 -0.126889456 # sulfoxide
2 OY 1.480 0.170 1.678 1.480 0.001000000 -0.126889456 # sulfonamide,sulfamide
2 O* 1.450 0.140 1.645 1.450 0.001000000 -0.126889456 # default O
3 N 1.625 0.170 1.810 1.600 0.054801302 -1.445846770 # amides
3 NY2 1.640 0.170 1.925 1.700 0.054801302 -2.445846770 # guanidine, etc.
3 NY 1.625 0.170 2.112 1.875 0.051222218 -2.220205820 # guanidine, etc.
3 NT 1.650 0.170 1.865 1.650 0.051222218 -2.220205820 # amines
3 NT2 1.650 0.170 2.112 1.875 0.051222218 -2.220205820 # amines
3 NT3 1.650 0.170 1.905 1.686 0.051222218 -2.220205820 # amines
3 NO 1.625 0.120 1.865 1.650 0.020864068 -0.347800883 # nitro N
3 NZ 1.640 0.170 2.250 2.000 0.024786691 -1.117108600 # nitrile N
3 NA 1.625 0.170 1.865 1.650 0.001000000 -0.511443539 # aromatic N
3 NA2 1.625 0.170 1.800 1.600 0.001000000 -0.511443539 # aromatic N
3 NAP 1.625 0.170 1.975 1.750 0.001000000 -0.511443539 # ionic aromatic N
3 NP00 1.625 0.170 1.948 1.725 0.003973653 1.685851020 # NH4+
3 NP0 1.625 0.170 2.008 1.780 0.003973653 1.685851020 # NH3+, etc.
3 NP1 1.625 0.170 2.195 1.950 0.003973653 1.685851020 # NH3+, etc.
3 NP 1.625 0.170 2.290 2.036 0.003973653 1.685851020 # NH3+, etc.
3 N* 1.650 0.170 1.865 1.650 0.005000000 -0.511443539 # default N
3 NN 1.650 0.170 1.837 1.625 0.005000000 0.000000000 # NN bridge
4 S 1.800 0.355 2.030 1.800 0.025682759 -1.666211680 # Sulfides, thiols
4 SY 1.775 0.250 2.002 1.775 0.025682759 -1.666211680 # sulfonamide, sulfamide
4 SZ 1.780 0.395 2.008 1.780 0.025682759 -1.666211680 # sulfoxide
4 SA 1.800 0.355 2.030 2.125 0.025682759 -1.666211680 # terminal S
4 S* 1.800 0.355 2.030 1.800 0.025682759 -1.666211680 # default S
5 HC 1.250 0.030 1.425 1.250 0.008598240 0.268726247 # H on aliphatic C
5 HC7 1.210 0.015 1.381 1.210 0.008598240 0.268726247 # H on aliphatic C
5 HC9 1.250 0.030 1.645 1.450 0.008598240 0.268726247 # H on aliphatic C
5 HA 1.210 0.030 1.381 1.210 0.030040813 0.268726247 # H on aromatic C
5 H 0.000 0.000 0.996 0.860 0.030040813 -0.651083722 # H on polar atom
5 HN 0.000 0.000 1.590 1.400 0.030040813 -0.651083722 # H on polar atom
5 H* 1.250 0.030 1.425 1.250 0.008598240 0.268726247 # default H
6 F 1.470 0.061 2.498 2.225 0.001000000 0.985400000 # F
6 Cl 1.700 0.300 2.195 1.950 0.001000000 0.320982824 # Cl
6 Br 1.735 0.470 2.800 2.500 0.001000000 -0.686339560 # Br
6 I 1.875 0.060 2.112 1.875 0.001000000 -0.848554734 # I
7 P2 1.875 0.200 2.107 1.870 0.005000000 0.000000000 # P
8 DF 0.000 0.000 1.500 1.250 0.005000000 0.000000000 # default
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