Code link: GitHub - masrul/GenTopo
For non-standard Force-field (which cannot be invoked through pdb2gmx), this tool can be used to generate gromacs topology template. It uses slightly different approach than x2top. It requires a PDB file of the molecule, which has two extra entries after the 80th column/character respectively atomTypes and charges. An example PDB file can be found in Example/test.pdb. It is recommended to have connectivity information in the PDB file, but not mandatory. If connectivity is missing, then the code will generate connectivity information using the heuristic of Van der Waals radius of atoms. In addition to internal coordinates, it also creates all required bondTypes, angleTypes, and dihedralTypes. GenTopo is independent of particular force filed, it simply creates template. User needs to provide required parameters once template is created. An example topology template created by GenTopo can be found in Example/topol.top.
# File name: Example/test.py # python test.py from GenTopo.Coord import PDBobj from GenTopo.Graph import MolGraph from GenTopo.GMXTopo import Topo # load a PDB file mol = PDBobj("test.pdb") # Create a Molecular Graph for generating bond, angles, dihedral etc. graph = MolGraph(mol, guessImpropers=True) # Now create gromacs topology by passing mol and graph gmx = Topo(mol, graph) # write topology file gmx.write("topol.top")
PDB to gromacs template
Generates internal coordinates
- Pairs (1-4)
- Improper dihedrals (for aromatic molecule)
- Bonds types
- Angle types
- Dihedral types
Support periodic molecule
git clone https://github.com/masrul/GenTopo cd GenTopo pip install .
Contact Person: Masrul Huda