Hi Valentina, Use pdb2gmx -ter
Cheers, Tsjerk On Wed, Feb 13, 2013 at 1:22 PM, Valentina Erastova <valentina.erast...@durham.ac.uk> wrote: > Hello! > > I am simulating Aspartate at pH > 10, so it needs to be fully deprotonated > (COO-, COO- and NH2). > > pdb2gmx allows to easily set side chains to be deprotanted, but is there a > straightforward way to make NH2, not NH3+? > > Thank you very much! > > > Kind regards, > Valentina > > __________________________ > Dr Valentina Erastova > > Postdoctoral Research Assistant > Department of Earth Sciences > Durham University > > Editor-in-Chief, > Kaleidoscope > > +44 786 131 6686 > > -- > 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/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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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/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
