Dear P.R.Anand Narayanan, > 1. how did the number of atoms and residues change.
Hydrogen atoms were added to your structure, which accounts for the increase in number of atoms. The number of residues should not have changed. Probably there is a discrepancy between the number of residues you have in your input file and the number of residues you expect to have in it. Maybe there are two residues missing from the list of coordinates? > 2. while pasting the HETATMS of the cofactors and the related molecules > necessary in the newly created pdb file (from that separate file), I changed > the changed the number of atoms accordingly (that is numbers starting from > 4454 to numbers starting from 5658). My question is that whether i should > change the numbers of the residues also accordingly???? since the numbering > of residues of cofactors and other necessary molecules werent in the > sequentially ordered number..... It's not necessary. From the MD point of view residue/atom numbering is fully arbitrary, as long as your topology is consistent and matches the atoms in the structure file. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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/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/mailing_lists/users.php