[gmx-users] energy minimization

marzieh dehghan dehghanmarzieh at gmail.com
Mon Sep 23 09:08:01 CEST 2013

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, but
after energy minimization, two chains are separated.

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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