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Major changes to ffld parsing/conversion.
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I reverted to the "resname.ATOMNAME" format for atom_types (Q6 will not
support character lengths > 8).
This will produce bigger parameter files since each topology element will have
it's own parameter definition. Cleaner format though, imo.

Fixed the tests and added a ffld14 test (ffld11 is anyhow deprecated and
cannot be used with non-ancient Schrodinger suites).

Added a Q to Gromacs conversion script in the form of a Ipython
Notebook (docs/examples/q2gmx/q2gmx.ipynb).

Renamed 'periodicity' to 'multiplicity' throughout the code.
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Miha Purg committed Jul 3, 2017
1 parent 76475e9 commit 6aa3d3e
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43 changes: 43 additions & 0 deletions docs/examples/q2gmx/fnl.lib
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# Generated with q_ffld2q.py, version 0.5.7
# Date: Mon Jul 3 17:36:04 2017
#
{FNL}
[atoms]
1 C1 fnl.C1 0.150000
2 C2 fnl.C2 -0.115000
3 C3 fnl.C3 -0.115000
4 C4 fnl.C4 -0.115000
5 C5 fnl.C5 -0.115000
6 C6 fnl.C6 -0.115000
7 O1 fnl.O1 -0.585000
8 H1 fnl.H1 0.115000
9 H2 fnl.H2 0.115000
10 H3 fnl.H3 0.115000
11 H4 fnl.H4 0.115000
12 H5 fnl.H5 0.115000
13 H6 fnl.H6 0.435000
[bonds]
C1 C2
C1 C6
C1 O1
C2 C3
C2 H1
C3 C4
C3 H2
C4 C5
C4 H3
C5 C6
C5 H4
C6 H5
O1 H6
[impropers]
C2 C1 C6 O1
C1 C2 C3 H1
C2 C3 C4 H2
C3 C4 C5 H3
C4 C5 C6 H4
C1 C6 C5 H5
[charge_groups]
C1 C2 C3 C4 C5 C6 O1 H1 H2 H3 H4 H5 H6
*--------------------------------------------------------------------------------

13 changes: 13 additions & 0 deletions docs/examples/q2gmx/fnl.pdb
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HETATM 1 C1 FNL 1 1.405 -0.000 0.000 1.00 0.00 C
HETATM 2 C2 FNL 1 0.702 1.216 0.000 1.00 0.00 C
HETATM 3 C3 FNL 1 -0.702 1.216 0.000 1.00 0.00 C
HETATM 4 C4 FNL 1 -1.404 -0.000 0.000 1.00 0.00 C
HETATM 5 C5 FNL 1 -0.702 -1.216 0.000 1.00 0.00 C
HETATM 6 C6 FNL 1 0.702 -1.216 0.000 1.00 0.00 C
HETATM 7 O1 FNL 1 2.769 -0.000 0.000 1.00 0.00 O
HETATM 8 H1 FNL 1 1.254 2.172 0.000 1.00 0.00 H
HETATM 9 H2 FNL 1 -1.254 2.172 0.000 1.00 0.00 H
HETATM 10 H3 FNL 1 -2.508 -0.000 0.000 1.00 0.00 H
HETATM 11 H4 FNL 1 -1.254 -2.172 0.000 1.00 0.00 H
HETATM 12 H5 FNL 1 1.254 -2.172 0.000 1.00 0.00 H
HETATM 13 H6 FNL 1 3.035 -0.920 0.000 1.00 0.00 H
93 changes: 93 additions & 0 deletions docs/examples/q2gmx/fnl.prm
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# Generated with q_ffld2q.py, version 0.5.7
# Date: Mon Jul 3 17:36:04 2017
#
[options]


[atom_types]
fnl.C1 1059.1297 1059.1297 23.6736 748.9178 16.7398 12.011 # FFLD: CA_C4_145 Benzene C - 12 site JACS,112,4768-90
fnl.C2 1059.1297 1059.1297 23.6736 748.9178 16.7398 12.011 # FFLD: CA_C4_145 Benzene C - 12 site JACS,112,4768-90
fnl.C3 1059.1297 1059.1297 23.6736 748.9178 16.7398 12.011 # FFLD: CA_C4_145 Benzene C - 12 site JACS,112,4768-90
fnl.C4 1059.1297 1059.1297 23.6736 748.9178 16.7398 12.011 # FFLD: CA_C4_145 Benzene C - 12 site JACS,112,4768-90
fnl.C5 1059.1297 1059.1297 23.6736 748.9178 16.7398 12.011 # FFLD: CA_C4_145 Benzene C - 12 site JACS,112,4768-90
fnl.C6 1059.1297 1059.1297 23.6736 748.9178 16.7398 12.011 # FFLD: CA_C4_145 Benzene C - 12 site JACS,112,4768-90
fnl.H1 69.5797 69.5797 4.9095 49.2003 3.4715 1.0079 # FFLD: HA_H6_146 Benzene H - 12 site JACS,112,4768-90
fnl.H2 69.5797 69.5797 4.9095 49.2003 3.4715 1.0079 # FFLD: HA_H6_146 Benzene H - 12 site JACS,112,4768-90
fnl.H3 69.5797 69.5797 4.9095 49.2003 3.4715 1.0079 # FFLD: HA_H6_146 Benzene H - 12 site JACS,112,4768-90
fnl.H4 69.5797 69.5797 4.9095 49.2003 3.4715 1.0079 # FFLD: HA_H6_146 Benzene H - 12 site JACS,112,4768-90
fnl.H5 69.5797 69.5797 4.9095 49.2003 3.4715 1.0079 # FFLD: HA_H6_146 Benzene H - 12 site JACS,112,4768-90
fnl.H6 0.0054 0.0054 0.0433 0.0038 0.0306 1.0079 # FFLD: HO_H8_240 H(O): alcohols
fnl.O1 690.3744 690.3744 23.86 488.1684 16.8716 15.999 # FFLD: OH_O6_167 O: phenol

[bonds]
fnl.C1 fnl.C2 938.0 1.4 # FFLD: high 0 => 0 CA-CA ==> CA-CA
fnl.C1 fnl.C6 938.0 1.4 # FFLD: high 0 => 0 CA-CA ==> CA-CA
fnl.C1 fnl.O1 900.0 1.364 # FFLD: high 0 => 0 CA-OH ==> OH-CA
fnl.C2 fnl.C3 938.0 1.4 # FFLD: high 0 => 0 CA-CA ==> CA-CA
fnl.C2 fnl.H1 734.0 1.08 # FFLD: high 0 => 0 CA-HA ==> HA-CA
fnl.C3 fnl.C4 938.0 1.4 # FFLD: high 0 => 0 CA-CA ==> CA-CA
fnl.C3 fnl.H2 734.0 1.08 # FFLD: high 0 => 0 CA-HA ==> HA-CA
fnl.C4 fnl.C5 938.0 1.4 # FFLD: high 0 => 0 CA-CA ==> CA-CA
fnl.C4 fnl.H3 734.0 1.08 # FFLD: high 0 => 0 CA-HA ==> HA-CA
fnl.C5 fnl.C6 938.0 1.4 # FFLD: high 0 => 0 CA-CA ==> CA-CA
fnl.C5 fnl.H4 734.0 1.08 # FFLD: high 0 => 0 CA-HA ==> HA-CA
fnl.C6 fnl.H5 734.0 1.08 # FFLD: high 0 => 0 CA-HA ==> HA-CA
fnl.H6 fnl.O1 1106.0 0.945 # FFLD: high 0 => 0 OH-HO ==> OH-HO

[angles]
fnl.C1 fnl.C2 fnl.C3 126.0 120.0 # FFLD: high 0 CA-CA-CA ==> CA-CA-CA
fnl.C1 fnl.C2 fnl.H1 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA
fnl.C1 fnl.C6 fnl.C5 126.0 120.0 # FFLD: high 0 CA-CA-CA ==> CA-CA-CA
fnl.C1 fnl.C6 fnl.H5 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA
fnl.C1 fnl.O1 fnl.H6 70.0 113.0 # FFLD: high 0 CA-OH-HO ==> HO-OH-CA
fnl.C2 fnl.C1 fnl.C6 126.0 120.0 # FFLD: high 0 CA-CA-CA ==> CA-CA-CA
fnl.C2 fnl.C1 fnl.O1 140.0 120.0 # FFLD: high 0 CA-CA-OH ==> OH-CA-CA
fnl.C2 fnl.C3 fnl.C4 126.0 120.0 # FFLD: high 0 CA-CA-CA ==> CA-CA-CA
fnl.C2 fnl.C3 fnl.H2 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA
fnl.C3 fnl.C2 fnl.H1 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA
fnl.C3 fnl.C4 fnl.C5 126.0 120.0 # FFLD: high 0 CA-CA-CA ==> CA-CA-CA
fnl.C3 fnl.C4 fnl.H3 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA
fnl.C4 fnl.C3 fnl.H2 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA
fnl.C4 fnl.C5 fnl.C6 126.0 120.0 # FFLD: high 0 CA-CA-CA ==> CA-CA-CA
fnl.C4 fnl.C5 fnl.H4 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA
fnl.C5 fnl.C4 fnl.H3 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA
fnl.C5 fnl.C6 fnl.H5 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA
fnl.C6 fnl.C1 fnl.O1 140.0 120.0 # FFLD: high 0 CA-CA-OH ==> OH-CA-CA
fnl.C6 fnl.C5 fnl.H4 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA

[torsions]
fnl.C1 fnl.C2 fnl.C3 fnl.C4 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-CA ==> CA-CA-CA-CA
fnl.C1 fnl.C2 fnl.C3 fnl.H2 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-HA ==> HA-CA-CA-CA
fnl.C1 fnl.C6 fnl.C5 fnl.C4 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-CA ==> CA-CA-CA-CA
fnl.C1 fnl.C6 fnl.C5 fnl.H4 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-CA ==> HA-CA-CA-CA
fnl.C2 fnl.C1 fnl.C6 fnl.C5 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-CA ==> CA-CA-CA-CA
fnl.C2 fnl.C1 fnl.C6 fnl.H5 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-HA ==> HA-CA-CA-CA
fnl.C2 fnl.C1 fnl.O1 fnl.H6 0.841 2.0 180.0 1.0 # FFLD: high 0 CA-CA-OH-HO ==> HO-OH-CA-CA
fnl.C2 fnl.C3 fnl.C4 fnl.C5 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-CA ==> CA-CA-CA-CA
fnl.C2 fnl.C3 fnl.C4 fnl.H3 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-HA ==> HA-CA-CA-CA
fnl.C3 fnl.C2 fnl.C1 fnl.C6 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-CA ==> CA-CA-CA-CA
fnl.C3 fnl.C2 fnl.C1 fnl.O1 3.625 2.0 180.0 1.0 # FFLD: high 0 OH-CA-CA-CA ==> OH-CA-CA-CA
fnl.C3 fnl.C4 fnl.C5 fnl.C6 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-CA ==> CA-CA-CA-CA
fnl.C3 fnl.C4 fnl.C5 fnl.H4 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-HA ==> HA-CA-CA-CA
fnl.C4 fnl.C3 fnl.C2 fnl.H1 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-CA ==> HA-CA-CA-CA
fnl.C4 fnl.C5 fnl.C6 fnl.H5 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-HA ==> HA-CA-CA-CA
fnl.C5 fnl.C4 fnl.C3 fnl.H2 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-CA ==> HA-CA-CA-CA
fnl.C5 fnl.C6 fnl.C1 fnl.O1 3.625 2.0 180.0 1.0 # FFLD: high 0 OH-CA-CA-CA ==> OH-CA-CA-CA
fnl.C6 fnl.C1 fnl.C2 fnl.H1 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-HA ==> HA-CA-CA-CA
fnl.C6 fnl.C1 fnl.O1 fnl.H6 0.841 2.0 180.0 1.0 # FFLD: high 0 CA-CA-OH-HO ==> HO-OH-CA-CA
fnl.C6 fnl.C5 fnl.C4 fnl.H3 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-CA ==> HA-CA-CA-CA
fnl.H1 fnl.C2 fnl.C1 fnl.O1 3.625 2.0 180.0 1.0 # FFLD: high 0 OH-CA-CA-HA ==> OH-CA-CA-HA
fnl.H1 fnl.C2 fnl.C3 fnl.H2 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-HA ==> HA-CA-CA-HA
fnl.H2 fnl.C3 fnl.C4 fnl.H3 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-HA ==> HA-CA-CA-HA
fnl.H3 fnl.C4 fnl.C5 fnl.H4 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-HA ==> HA-CA-CA-HA
fnl.H4 fnl.C5 fnl.C6 fnl.H5 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-HA ==> HA-CA-CA-HA
fnl.H5 fnl.C6 fnl.C1 fnl.O1 3.625 2.0 180.0 1.0 # FFLD: high 0 OH-CA-CA-HA ==> OH-CA-CA-HA

[impropers]
fnl.C1 fnl.C2 fnl.C3 fnl.H1 1.1 180.0 # FFLD: high aromatic atom
fnl.C1 fnl.C6 fnl.C5 fnl.H5 1.1 180.0 # FFLD: high aromatic atom
fnl.C2 fnl.C1 fnl.C6 fnl.O1 4.0 180.0 # FFLD: high aromatic atom
fnl.C2 fnl.C3 fnl.C4 fnl.H2 1.1 180.0 # FFLD: high aromatic atom
fnl.C3 fnl.C4 fnl.C5 fnl.H3 1.1 180.0 # FFLD: high aromatic atom
fnl.C4 fnl.C5 fnl.C6 fnl.H4 1.1 180.0 # FFLD: high aromatic atom

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