I am doing a minimization for P-glycoprotein in GROMACS and the topology database seems to be missing an 'HG' residue. I've edited the residues.da in the topology file to add HG, but I'm still getting the same error.
Giancarlos Ortega
Apparently, you are trying to use a protein with hydrogens atoms and a different nomenclature to those added by pdb2gmx tool... try to run pdb2gmx and add the flag "-ignh"... this way, pdb2gmx will ignore any hydrogen atom in your structure and add hydrogens accordingly... be aware that you will have to specify the protonation states of histidines, etc, etc...
I assume you don't have any residue/ligand who is not present in the force field...
hope this helps!
It seems you need to add the force fields of your glycans into topol.top, you can generate them with PRODRG server http://prodrg1.dyndns.org/prodrg_lic.html
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