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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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