Re: [gmx-users] calculation of distance between the center of geometry of two proteins
thank you so much for your reply. On 5/28/18, Soham Sarkar 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 > 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 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 wrote: >> >> Delete from -select.. previous are ok >> >> >> >> On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, >> 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 * 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.
Re: [gmx-users] calculation of distance between the center of geometry of two proteins
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 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 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 wrote: > >> Delete from -select.. previous are ok > >> > >> On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, > 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.
Re: [gmx-users] calculation of distance between the center of geometry of two proteins
Hi, g_dist does not take selection arguments so you cannot use -select or anything that was an argument to it. You can either rely on the default selections that all GROMACS tools make if there is no index file, or use e.g. g_select to make an index file with the selections you want. Note that gmx distance in more recent versions of GROMACS has the -select keyword, which you should probably install and use :-) Mark On Mon, May 28, 2018, 11:55 SHAHEE ISLAM 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 wrote: > > Delete from -select.. previous are ok > > > > On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, > 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. > -- 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.
Re: [gmx-users] calculation of distance between the center of geometry of two proteins
The command should be g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg Then select Chain_A and Chain_B as per the indexing number On Mon, May 28, 2018 at 3:24 PM, SHAHEE ISLAM 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 wrote: > > Delete from -select.. previous are ok > > > > On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, > 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.
Re: [gmx-users] calculation of distance between the center of geometry of two proteins
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 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 wrote: >> Delete from -select.. previous are ok >> >> On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, 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.
Re: [gmx-users] calculation of distance between the center of geometry of two proteins
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 wrote: > Delete from -select.. previous are ok > > On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, 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.
Re: [gmx-users] calculation of distance between the center of geometry of two proteins
Delete from -select.. previous are ok On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, 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.
[gmx-users] calculation of distance between the center of geometry of two proteins
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.
