I read that. but while executing tpbconv i did not see where i can specify that i do not want solvent?
Thanks Kavya On Thu, Jul 12, 2012 at 5:47 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > On 7/12/12 8:15 AM, Kavyashree M wrote: >> >> Dear Sir, >> >> I had a problem again during g_saltbr calculation it needs >> .xtc and .tpr file, I can reduce the .xtc file to have only >> protein but .tpr file will have water also in it. inorder to generate >> new tpr file without water using grompp, i need topology file >> without water .. so do you suggest me to go this way.. it >> appears quite complicated! >> > > In fact, it's quite easy with tpbconv. From tpbconv -h: > > "3. by creating a .tpx file for a subset of your original tpx file, which is > useful when you want to remove the solvent from your .tpx file, or when you > want to make e.g. a pure Calpha .tpx file. Note that you may need to use > -nsteps -1 (or similar) to get this to work. WARNING: this .tpx file is not > fully functional." > > > -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