Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid
On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/18/13 12:35 PM, shahid nayeem wrote: >> >> Hi >> Is it possible to write .top file from .xtc and .tpr using index.ndx >> so that .top is available for tailormade components of simulated >> protein. >> > > All topology information is in the .tpr, but not in .top format. You may be > able to post-process the output of gmxdump to produce some hacked version, > but that's just a bit of a hand-waving guess. I don't really understand > what your objective is. > > -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 > * 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 * 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
