Dear Gromacs Users, I have simulated a protein -ligand complex in the popc bilayer and while analysing the results i want to find distance between two residues in the protein during simulation. For that I think I have to use g_hbond command by creating an index.file containing the new groups, but while creating the new index file I could select groups , but unable to save them using 'q' command. jhcdyprod31ns.gro is the output file after simulation for a period of time.
I executed the command: make_ndx -f jhcdyprod31ns.gro -o output.ndx * then i got the following options,* Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 539 Protein residues There are: 5 Ion residues There are: 133 Other residues There are: 15828 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 62876 atoms 1 Protein : 8470 atoms 2 Protein-H : 4235 atoms 3 C-alpha : 539 atoms 4 Backbone : 1617 atoms 5 MainChain : 2157 atoms 6 MainChain+Cb : 2652 atoms 7 MainChain+H : 2675 atoms 8 SideChain : 5795 atoms 9 SideChain-H : 2078 atoms 10 Prot-Masses : 8470 atoms 11 non-Protein : 54406 atoms 12 Ion : 5 atoms 13 NA : 2 atoms 14 CL : 1 atoms 15 LIG : 53 atoms 16 POPC : 6864 atoms 17 CL- : 2 atoms 18 Other : 6917 atoms 19 NA : 2 atoms 20 CL : 1 atoms 21 LIG : 53 atoms 22 POPC : 6864 atoms 23 CL- : 2 atoms 24 Water : 47484 atoms 25 SOL : 47484 atoms 26 non-Water : 15392 atoms 27 Water_and_ions : 47489 atoms nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom & 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index * but, i wanted to create a new group, so i selected a residue number 15 and verified it as a new group added in the index file, this was ok *> r15 28 r_15 : 12 atoms* > 0 System : 62876 atoms 1 Protein : 8470 atoms 2 Protein-H : 4235 atoms 3 C-alpha : 539 atoms 4 Backbone : 1617 atoms 5 MainChain : 2157 atoms 6 MainChain+Cb : 2652 atoms 7 MainChain+H : 2675 atoms 8 SideChain : 5795 atoms 9 SideChain-H : 2078 atoms 10 Prot-Masses : 8470 atoms 11 non-Protein : 54406 atoms 12 Ion : 5 atoms 13 NA : 2 atoms 14 CL : 1 atoms 15 LIG : 53 atoms 16 POPC : 6864 atoms 17 CL- : 2 atoms 18 Other : 6917 atoms 19 NA : 2 atoms 20 CL : 1 atoms 21 LIG : 53 atoms 22 POPC : 6864 atoms 23 CL- : 2 atoms 24 Water : 47484 atoms 25 SOL : 47484 atoms 26 non-Water : 15392 atoms 27 Water_and_ions : 47489 atoms 28 r_15 : 12 atoms then**, i save it with q command *> q Back Off! I just backed up output.ndx to ./#output.ndx.15# but, when i wanted to add another group to this index file i again i could not see the first new group added i.e. it has the default groups, the new groups added are not saved. Please let know your suggestions to overcome this error. Thanks, ram * *
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