[gmx-users] postdocking MD?

[Anton Feenstra]

"Peter C. Lai" wrote:
> 
> Sorry for being a newbie, but I am trying to use gromacs
> to look at ligand-receptor interaction. I generated
> coordinates for the ligand via a docking program and I merged
> them with the receptor pdb. The ligand is listed as UNK in the pdb,
> and pdb2gmx doesn't like it (unknown residue UNK).
> Should I alter to pdb to list the ligand as a heteroatom record?
> What is the best way to go about this? The documentation covers
> MD of a single protein in a solvent; I'm trying to get a trajectory
> of a ligand in its binding pocket...

Your problem probably lies in another direction: you will need a
forcefield/topology description of your ligand. Chances are that it
is not (yet) available in the topology database(s) for any of the
forcefields available in Gromacs. The PRODRG web-server can build a
good starting point for your topology, the forcefield you will have
to make yourself. There is an entry in the FAQ that covers the next 
step of generating a protein/ligand topology.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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