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.* -- 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
