Dear GMX users I am trying to make an index.ndx file of my complex which includes a receptor and a peptide using this command:
gmx make_ndx -f em.gro -o index.ndx Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 330 Protein residues There are: 15278 Water residues There are: 7 Ion residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 51172 atoms 1 Protein : 5331 atoms 2 Protein-H : 2659 atoms 3 C-alpha : 330 atoms 4 Backbone : 990 atoms 5 MainChain : 1322 atoms 6 MainChain+Cb : 1633 atoms 7 MainChain+H : 1639 atoms 8 SideChain : 3692 atoms 9 SideChain-H : 1337 atoms 10 Prot-Masses : 5331 atoms 11 non-Protein : 45841 atoms 12 Water : 45834 atoms 13 SOL : 45834 atoms 14 non-Water : 5338 atoms 15 Ion : 7 atoms 16 NA : 7 atoms 17 Water_and_ions : 45841 atoms nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index > splitch 1 Found 10 chains 1: 189 atoms (1 to 189) 2: 108 atoms (190 to 297) 3: 283 atoms (298 to 580) 4: 130 atoms (581 to 710) 5: 173 atoms (711 to 883) 6: 10 atoms (884 to 893) 7: 4087 atoms (894 to 4980) 8: 99 atoms (4981 to 5079) 9: 125 atoms (5080 to 5204) 10: 127 atoms (5205 to 5331) I dont know it found 10 chains instead of finding 2 chains ( chain A and chain B).How can I make the desired index file composed of:18 protein chain A19 protein chain B best regardsFarial -- 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.