thank you so much for your reply. On 5/28/18, Soham Sarkar <soham9...@gmail.com> wrote: > use the latest .tpr formed after production run else try > > tpbconv -s dynamic.tpr -o dynamic_new.tpr > > On Mon, May 28, 2018 at 3:29 PM, SHAHEE ISLAM <islamsha...@gmail.com> > wrote: > >> thank you so much. >> after deleting from -select its now working.but the fatal error is >> Molecule in topology has atom numbers below and above natoms (565). >> You are probably trying to use a trajectory which does not match the >> first 565 atoms of the run input file. >> You can make a matching run input file with tpbconv. >> >> >> On 5/28/18, SHAHEE ISLAM <islamsha...@gmail.com> wrote: >> > after deleting -select >> > this error is coming >> > Invalid command line argument: >> > cog of group "Chain_A" plus cog of group "Chain_B" >> > >> > >> > On 5/28/18, Soham Sarkar <soham9...@gmail.com> wrote: >> >> Delete from -select.. previous are ok >> >> >> >> On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, <islamsha...@gmail.com> >> wrote: >> >> >> >>> hi, >> >>> to calculate the distance between the center of geometry of two >> >>> proteins, i am using this command >> >>> g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg >> >>> -select 'cog of group "Chain_A" plus cog of group "Chain_B"' >> >>> Invalid command line argument: >> >>> -select >> >>> here in this index file the two chain group name Chain_A and Chain_B >> >>> how i will select the two chain. >> >>> >> >>> thanking you >> >>> shahee islam >> >>> university of calcutta >> >>> -- >> >>> Gromacs Users mailing list >> >>> >> >>> * Please search the archive at >> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> >>> posting! >> >>> >> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >>> >> >>> * For (un)subscribe requests visit >> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> >>> send a mail to gmx-users-requ...@gromacs.org. >> >>> >> >> -- >> >> Gromacs Users mailing list >> >> >> >> * Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> >> posting! >> >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> * For (un)subscribe requests visit >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send >> >> a >> >> mail to gmx-users-requ...@gromacs.org. >> >> >> > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > > > -- > SOHAM SARKAR > Junior Research Fellow > Department of Chemistry > INDIAN INSTITUTE OF TECHNOLOGY BOMBAY > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list
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