[gmx-users] energy minimization
mark.j.abraham at gmail.com
Mon Sep 23 15:55:48 CEST 2013
On Sep 23, 2013 9:08 AM, "marzieh dehghan" <dehghanmarzieh at gmail.com> 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.
> 2- insulin contains two chains (A & B) which connect by disulfide bond,
> after energy minimization, two chains are separated.
Did pdb2gmx even report it being made?
> I would like to know how to solve these problems?
> best regards
> *Marzieh Dehghan
> PhD Candidate of Biochemistry
> Institute of biochemistry and Biophysics (IBB)
> University of Tehran, Tehran- Iran.*
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