There is only one Cystein:
ATOM 1797 N CYS A 211 10.568 1.888 4.891 1.00 1.00 ATOM 1798 CA CYS A 211 11.782 1.312 5.391 1.00 1.00 ATOM 1799 CB CYS A 211 12.968 1.606 4.452 1.00 1.00 ATOM 1800 SG CYS A 211 14.599 1.282 5.172 1.00 1.00 ATOM 1801 C CYS A 211 12.106 1.904 6.723 1.00 1.00 ATOM 1802 O CYS A 211 12.427 1.169 7.655 1.00 1.00 Eva > > > On 7/19/12 6:17 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi Justin, >> thank you for your answer. >> I already tried the -ss command but nothing happens. The program just >> writes the topology file but it does not ask me anything. My command >> was: >> >> pdb2gmx -f protOnly.pdb -o 3m71.gro -p 3m71.top -ss -water tip3p -ff >> amber03 >> >> is there something wrong with this command? > > No, it's fine. How many cysteines are in the structure? > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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