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.
