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.
