Ok may be i need to specify an index file. I will try that. And regarding the WARNING: this .tpx file is not fully functional. I hope it will work fine enough to finish g_saltbr calculation?
Thanks Kavya On Thu, Jul 12, 2012 at 5:59 PM, Kavyashree M <hmkv...@gmail.com> wrote: > 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