Thank you, Mark. I understand from your suggestion, that what I got from topology and solvation phases is correct, and MD simulations even if it affects the numbering of the structure but the simulation results remain unaffected and I could renumber my residues at the end of simulation as it should be.
This the first time I'm facing this case as it's the first time I'm running MD simulation of a protein complex. Khadija *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics Phone: 33339584 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
