[gmx-users] Reg : Simulating heterologous protein complex with bound ligand

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 24 23:17:47 CET 2011

Rohit Farmer wrote:
> Dear Gromacs Users,
> I am working on a protein complex with two subunits which are 
> heterologous and I docked them using HADDOCK. Now, to one of the subunit 
> I built a ligand covalently attached to one of the residue, which enters 
> into the active site of the another subunit in the complex.
> Now I want to simulate the entire complex i.e. the two subunits and the 
> bound ligand. Does anyone know how it can be done.

Multiple proteins should be automatically processed with pdb2gmx, provided you 
give some indication where new chains should start (see pdb2gmx -chainsep for 
options).  Novel residues have to be parameterized and implemented in the parent 
force field.  See:




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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