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? Best, Eva > > > On 7/19/12 5:00 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> I want to add protonation states to my protein with pdb2gmx. >> I now that there are the options: >> >> -lys -arg -asp -glu -his >> >> to do this. >> >> But was is about the cystein. How can I protonate this one? >> Is there also an option for it which I haven't seen? >> > > The -ss flag controls cysteine protonation, in the sense that you can > toggle > between disulfide and free forms of cysteine. Some force fields include > an > anionic form of cysteine as well. > > -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