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

[Justin A. Lemkul]

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:

http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================