Hi, The "1" selects the first index group, which is the whole peptide. If you want to select the first residue, you have to use some other syntax.
Mark On Tue, Aug 22, 2017 at 6:50 PM Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > Hello, > I have a Diglycine peptide in .gro file as:- > 1GLY N 1 1.312 0.940 1.100 0.5173 0.1852 0.2665 > 1GLY H1 2 1.375 1.015 1.064 0.3308 -0.2009 -0.8897 > 1GLY H2 3 1.376 0.860 1.115 2.0625 0.7372 -2.9245 > 1GLY H3 4 1.242 0.907 1.031 0.2385 0.6317 0.3326 > 1GLY CA 5 1.240 0.963 1.228 0.3801 -0.0854 0.2381 > 1GLY HA1 6 1.155 0.898 1.233 1.2980 -1.3807 -0.5280 > 1GLY HA2 7 1.321 0.963 1.300 -1.1296 -1.6137 1.9682 > 1GLY C 8 1.185 1.101 1.232 0.0318 -0.2122 -0.1516 > 1GLY O 9 1.171 1.174 1.133 0.1199 0.2166 0.1513 > 2GLY N 10 1.148 1.148 1.352 -1.0777 -0.3721 -0.4264 > 2GLY HN 11 1.142 1.091 1.434 -0.1054 0.0667 -0.0362 > 2GLY CA 12 1.092 1.277 1.377 0.5476 0.2162 0.2355 > 2GLY HA1 13 1.170 1.351 1.365 0.3836 0.3441 -0.0427 > 2GLY HA2 14 1.012 1.294 1.306 -0.5941 1.1037 1.7136 > 2GLY C 15 1.031 1.298 1.514 0.2354 -0.4348 0.1971 > 2GLY OT1 16 0.923 1.238 1.541 0.2601 -0.2386 0.7420 > 2GLY OT2 17 1.091 1.369 1.598 0.1878 -0.0650 -0.0813 > > So now i want to index of the Nitrogen (N) of 1GLY only, but not N of > 2GLY... > > I tried the the following command as:- > gmx make_ndx -f abc.gro -o def.ndx > 1 & a N > > But it is giving 2 Protein_&_N : 2 atoms > which is taking the N of 2GLY too into consideration....which i don't > required, I need the N of ...1GLY only.... > > So what is the correct command for this..?? > > Thank you... > > > > With Best Regards, > > DILIP.H.N > Ph.D Student > > > > <https://mailtrack.io/> Sent with Mailtrack > < > https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22 > > > -- > 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.
