Desired feature/enhancement
The autotoppar option of the topoaa module allows to automatically generate top/param files for ligands calling prodrg. This however only works when the ligand is an isolated molecule (which is fine for protein-ligand docking).
It however fails if the ligand, e.g. a co-factor, is part of a protein, because the entire PDB file is passed to prodrg, which causes a failure.
The code should be change to extract the ligand coordinates and only pass those to prodrg.
It should also be able to handle multiple ligands.
Motivation
This will extends haddock's capabilities to deal with ligands and co-factors.
Description
- extract unknown ligands (only the 1st instance in case of multiple copies) and pass that to prodrg.
- if multiple different ligand are detected, each should be passed to prodrg and the resulting top/param files concatenated
- prodrg has a parameter that allows to define the character used to define the atom types. This should be unique one, not overlapping with what is in the cofactor.top file (which was created using prodrg) to avoid overlap in parameters definitions.
Desired feature/enhancement
The autotoppar option of the
topoaamodule allows to automatically generate top/param files for ligands calling prodrg. This however only works when the ligand is an isolated molecule (which is fine for protein-ligand docking).It however fails if the ligand, e.g. a co-factor, is part of a protein, because the entire PDB file is passed to prodrg, which causes a failure.
The code should be change to extract the ligand coordinates and only pass those to prodrg.
It should also be able to handle multiple ligands.
Motivation
This will extends haddock's capabilities to deal with ligands and co-factors.
Description