Parameters
The parameters are obtained automatically using SwissParam service (https://www.swissparam.ch). This is done in a seamlessly without user intervention. The molecular structure is transformed to .mol2 format and the connectivity is generated using OpenBabel library. Then the molecule is updated to SwissParam servers and the parameters are downloaded. This process requires internet connection and is usually very fast for small molecules.
Once the parameters are obtained, they are stored in a cache file (.parameters.pkl) in the working directory. This file can contain the parameters for multiple molecules and it is used for all calculations performed in the same directory. This file can be used to run calculations offline.
Custom parameters
In some cases, the parameters obtained from SwissParam servers are not suitable for the calculation. In this case, the user can provide custom parameters computed elsewhere. The custom parameters should be written in an gromacs .itp formatted file. Also it is necessary to include a .pdb formatted file of the structure with the same atom labels than the .itp file. Then the following function can be used to generate a .parameters.pkl file containing the parameters:
from gromorg.setparam import SetParams
from pyqchem.structure import Structure
# Initialize the SetParams with database file (append data if file exists)
data = SetParams(filename='.parameters.pkl')
# Add parameters to database
data.add_data('ethylene.itp', 'ethylene.pdb') # ethylene
An example is provided in the examples directory (https://github.com/abelcarreras/gromorg/blob/master/examples/set_params.py).
Example data
ethylene.itp
: ----
; Built itp for test.mol2
; by user vzoete Wed Jul 14 16:04:50 UTC 2021
; ----
;
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
C=C 6 12.0110 0.0 A 0.372396 0.284512
HCMM 1 1.0079 0.0 A 0.235197 0.092048
[ pairtypes ]
; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
[ moleculetype ]
; Name nrexcl
test 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 C=C 1 LIG C 1 -0.3000 12.0110
2 C=C 1 LIG C1 2 -0.3000 12.0110
3 HCMM 1 LIG H 3 0.1500 1.0079
4 HCMM 1 LIG H1 4 0.1500 1.0079
5 HCMM 1 LIG H2 5 0.1500 1.0079
6 HCMM 1 LIG H3 6 0.1500 1.0079
[ bonds ]
; ai aj fu b0 kb, b0 kb
1 2 1 0.13330 572403.8 0.13330 572403.8
1 3 1 0.10830 311344.8 0.10830 311344.8
1 4 1 0.10830 311344.8 0.10830 311344.8
2 5 1 0.10830 311344.8 0.10830 311344.8
2 6 1 0.10830 311344.8 0.10830 311344.8
[ pairs ]
; ai aj fu
3 5 1
3 6 1
4 5 1
4 6 1
[ angles ]
; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
2 1 3 1 121.0040 322.18 121.0040 322.18
2 1 4 1 121.0040 322.18 121.0040 322.18
3 1 4 1 119.5230 219.80 119.5230 219.80
1 2 5 1 121.0040 322.18 121.0040 322.18
1 2 6 1 121.0040 322.18 121.0040 322.18
5 2 6 1 119.5230 219.80 119.5230 219.80
[ dihedrals ]
; ai aj ak al fu phi0 kphi mult phi0 kphi mult
3 1 2 5 9 180.00 25.1040 2 180.00 25.1040 2
3 1 2 6 9 180.00 25.1040 2 180.00 25.1040 2
4 1 2 5 9 180.00 25.1040 2 180.00 25.1040 2
4 1 2 6 9 180.00 25.1040 2 180.00 25.1040 2
[ dihedrals ]
; ai aj ak al fu xi0 kxi xi0 kxi
1 3 2 4 2 0.00 3.6150 0.00 3.6150
2 5 1 6 2 0.00 3.6150 0.00 3.6150
#ifdef POSRES_LIGAND
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
2 1 1000 1000 1000
#endif
Note
Notice that moleculetype name must be test.
ethylene.pdb
REMARK FOR INFORMATIONS, PLEASE CONTACT:
REMARK ZOETE VINCENT
REMARK VINCENT.ZOETE_AT_ISB-SIB.CH
REMARK SWISS INSTITUTE OF BIOINFORMATICS
REMARK MOLECULAR MODELING GROUP
REMARK QUARTIER SORGE - BATIMENT GENOPODE
REMARK CH-1015 LAUSANNE
REMARK SWITZERLAND
REMARK T: +41 21 692 4082
REMARK ****************************************************************
REMARK DATE: 7/14/21 16: 4:50 CREATED BY USER: root
ATOM 1 C LIG 1 0.669 0.000 0.000 1.00 0.00 LIG
ATOM 2 C1 LIG 1 -0.669 0.000 0.000 1.00 0.00 LIG
ATOM 3 H LIG 1 1.232 0.929 0.000 1.00 0.00 LIG
ATOM 4 H1 LIG 1 1.232 -0.929 0.000 1.00 0.00 LIG
ATOM 5 H2 LIG 1 -1.232 0.929 0.000 1.00 0.00 LIG
ATOM 6 H3 LIG 1 -1.232 -0.929 0.000 1.00 0.00 LIG
TER 7 LIG 1
END