.. highlight:: rst 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: .. code-block:: python 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 ~~~~~~~~~~~~ .. code-block:: : ---- ; 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 ~~~~~~~~~~~~ .. code-block:: 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