On Sep 23, 2013 9:08 AM, "marzieh dehghan" <dehghanmarz...@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, but > after energy minimization, two chains are separated.
Did pdb2gmx even report it being made? Mark > 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.* > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
