[gmx-users] pdb2gmx and specbond with arbitrary ligand

[Leandro Bortot]

Dear users,

     I want to simulate some ligands covalently bonded to a protein, i.e.
covalent inhibitors. I've searched the list and found similar issues, but
mainly with heme in forcefields in which it is already supported. I use the
AMBER99SB-ILDN forcefield and I can simulate the non covalent complexes
with no problems using GAFF.

     I suppose I can just put both the ligand and the protein under the
same [moleculetype] specification in a .itp file and manually add the bonds
in this topology. It seems that I only need a script to renumber the atoms
to achieve this. However, I think pdb2gmx and specbond.dat may already be
able to do this. The problem is: How can pdb2gmx understand my arbitrary
ligand? Is adding my ligand to a local copy of
amber99sb-ildn/aminoacids.rtp the only way?

     What would be the best way to do that?


Thank you for your attention,
Leandro.