stefdoerr
commented
1 year ago If you want to build systems with custom ligands you need to get their parameters from somewhere. We currently provide a tool for generating small molecule parameters for AMBER forcefields which is parameterize https://www.playmolecule.com/parameterize/
If you want to instead produce an rtf/prm for CHARMM you will have to use match https://brooks.chem.lsa.umich.edu/index.php?matchserver=submit but we don't officially support CHARMM anymore due to licensing issues so my support might be slightly more limited.
suice07
Hey guys,
I am totally new to htmd and trying with those tutorials, I noticed that , in the" System building: Protein in Membrane with Ligand" section , the ligand with resname 'BEN' was seperated from the protein itself. and using the command below to build topology for the ligand.
topos_charmm = charmm.defaultTopo() + [join(datadir, 'BEN.rtf')] params_charmm = charmm.defaultParam() + [join(datadir, 'BEN.prm')]I did not have the .trf and .prm before that. how can I generated them? I notice that there is a function named
charmm.search,is it used for searching the topology files? what if there is no resname for the molecule I inserted to the protein?is there any simple way to build topology for the ligand-protein sovalted box ?when I use charmm.build for the whole complex, there is an error: "Info: generating structure...psfgen) unknown residue type BEN failed!" It will be really nice if any help was offered, thanks in advance