Hi. Mg is probably in the force field already. You don't need to run it through pdb2gmx. Add it manually after generation of the topology for the protein. #include "ions.itp" in the topology file and add the correct name (check ions.itp) under [ molecules ]. Be sure to have all atoms matching in order with your coordinate file.
Cheers, Tsjerk On Mon, Apr 13, 2009 at 6:34 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > akalabya bissoyi wrote: >> >> "hello gromacs, >> i am trying to simulate my protein ligand complex but my protein contains >> Mg ion and while running Gromacs error is coming in command pdb2gmx.It is >> not able to recognize Mg ion. >> I included the coordinates for Mg ion in protein pdb file.And when i >> included coordinates for Mg ion in ligand file , Prodrg server was showing >> error during generation of ligand toplogy file as it doesnt include Mg ion. >> So pls suggest me how can i do this job.." > > There is probably no straightforward clearly-correct approach. See > http://wiki.gromacs.org/index.php/Exotic_Species in the first instance. > > Mark > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://www.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 > -- 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://www.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
