Hello, I'm using GROMACS 5.1.13 and ran into a problem I've never encountered before. I've run a simulation on a zinc-finger DNA complex and defined a group in my index filed called "Protein_DNA" from the default "Protein" and "DNA" groups. This group should contain 4666 atoms, which it does.
$gmx make_ndx -n index.ndx 0 System : 180141 atoms 1 Protein : 2830 atoms <================== 2 Protein-H : 1427 atoms 3 C-alpha : 171 atoms 4 Backbone : 513 atoms 5 MainChain : 685 atoms 6 MainChain+Cb : 851 atoms 7 MainChain+H : 854 atoms 8 SideChain : 1976 atoms 9 SideChain-H : 742 atoms 10 Prot-Masses : 2830 atoms 11 non-Protein : 177311 atoms 12 Ion : 32 atoms 13 ZN : 7 atoms 14 NA : 25 atoms 15 DNA : 1836 atoms <================= 16 ZN : 7 atoms 17 NA : 25 atoms 18 Water : 175443 atoms 19 SOL : 175443 atoms 20 non-Water : 4698 atoms 21 Water_and_ions : 175475 atoms 22 Protein_DNA : 4666 atoms <================= I'm not sure why the ZN and NA groups show up twice, but I assume it's not an issue. Anyway, Protein_DNA is defined, and when I compare the values in the index.ndx file to the atom numbers in the .gro file, it all matches up. In my .mdp input file, I specify this group to be output as a compressed .xtc trajectory. ; OUTPUT CONTROL OPTIONS = nstxout = 10000 nstvout = 10000 nstfout = 0 nstlog = 10000 nstenergy = 2500 nstxout-compressed = 1000 compressed-x-precision = 1000 compressed-x-grps = Protein_DNA And then I run my simulation. I now have my traj.xtc file, which I want to process. However, when using gmx trjconv, and select the group Protein_DNA, I get the following error: $gmx trjconv -f traj.xtc -n index.ndx [options] Fatal error: Index[4659] 4667 is larger than the number of atoms in the trajectory file (4666). There is a mismatch in the contents of your -f, -s and/or -n files. The group DNA_Protein should contain 4666 atoms, and I've verified that my traj.xtc file indeed contains 4666 items with gmx check: $gmx check -f traj.xtc Checking file traj.xtc Reading frame 0 time 0.000 # Atoms 4666 ... So what is the problem here? The error message states that "Index[4659] 4667 is larger than the number of atoms in the trajectory file (4666)", which is true - the 4659th atom listed in the "Protein_DNA" index is indeed atom 4667, but so what? There's 4666 atoms in the index, and 4666 atoms in traj.xtc file - I don't see where the mismatch is. Can someone help me out with this and suggest some things to try, or explain what is wrong if I'm missing something? Is it possible this is related to the fact that the protein topology file includes 7 zinc atoms (since this is a ZF protein), which are not included in the group Protein_DNA? Note that if I don't supply an index file and choose "Protein" from the default groups, gmx trjconv will run, but if I choose "DNA", I get a similar error. Fatal error: Index[1829] 4667 is larger than the number of atoms in the trajectory file (4666). There is a mismatch in the contents of your -f, -s and/or -n files. -- 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.