[gmx-users] energy minimization

Justin Lemkul jalemkul at vt.edu
Mon Sep 23 14:03:50 CEST 2013

On 9/23/13 3:08 AM, marzieh dehghan wrote:
> Hi every body
> in order to protein- ligand docking, energy minimization was done by
> GROMACS. I did the following steps for insulin pdb file:
> 1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce
> 2- grompp -f em.mdp -c test.pdb -p topol.top -o em.tpr
> 3-mdrun -v -deffnm em
> 4- editconf -f em.gro -o final.pdb -c -d 1.0 -bt cubic
> everything was perfect, but the final pdb file has two problems:
> 1- chain ID was missed.

Chain IDs are irrelevant in Gromacs, but can be restored by converting file 
formats using trjconv and a .tpr file.

> 2- insulin contains two chains (A & B) which connect by disulfide bond, but
> after energy minimization, two chains are separated.

This may or may not be a simple PBC effect (again, fixed with trjconv).  If the 
bond exists in the topology, it cannot be broken.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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