Hi, Look at the contents of the .gro file with the "less" tool and see what the numbering is :-)
Mark On Wed, May 2, 2018 at 3:07 PM MD <refm...@gmail.com> wrote: > Hi Gromacs, > > I was trying to index two amino acids to two groups and calculate the > distance between them. > > I used the command > > "gmx make_ndx -f md.gro -o index.ndx" > > and tried to select residue 159 from chain A (group of r_159) and residue > 15 from chain B. However, when I used the "l" function to list all the > residues I was not able to find the residue 15 from chain B. I was able to > find it based on the sequence but it has a different number 372, instead of > 15 in its original structure of chain B. I think gromacs renumbered the > whole sequence and combined chain A and B? When I select r 372, i was told > it is an empty group. > > Can someone help me here, please? > > Thanks in advance, > > Ming > -- > 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.