Hi Abhijit, I think the Zinc ion goes with chain B and uses the same identifier. Given the fact that you didn't quite understand the error, and found it necessary to post a question, this raises another question: should you be wanting to simulate a protein with a zinc ion? (http://www.gromacs.org/WIKI-import/Exotic_Species).
Cheers, Tsjerk On Tue, Oct 6, 2009 at 5:02 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > abhijit kayal wrote: >> >> Hello everyone >> I am going to analysis the PDB file 3GJN.pdb.After giving the pdb2gmx it >> shows the fatal error >> >> "chain identifier 'B' was used in two non-sequential blocks (residue 404, >> atom 3227)".So what is the solution for this. >> > > The error message is quite clear, even telling you where the problem is! > > Make sure chain identifiers are continuous. Have you inserted or deleted > anything? Dealing with ligands or co-solvents that might be arranged oddly? > > -Justin > >> Thank you >> >> Abhijit >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-us...@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 > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-us...@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 > -- 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