Dear Gromacs Users,<br><br>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.<br>
<br>I executed the command:<br><br>make_ndx -f jhcdyprod31ns.gro -o output.ndx<br><i><br><b>then i got the following options,</b></i><br><br>Reading structure file<br>Going to read 0 old index file(s)<br>Analysing residue names:<br>
There are: 539 Protein residues<br>There are: 5 Ion residues<br>There are: 133 Other residues<br>There are: 15828 Water residues<br>Analysing Protein...<br>Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...<br>
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...<br><br> 0 System : 62876 atoms<br> 1 Protein : 8470 atoms<br> 2 Protein-H : 4235 atoms<br> 3 C-alpha : 539 atoms<br>
4 Backbone : 1617 atoms<br> 5 MainChain : 2157 atoms<br> 6 MainChain+Cb : 2652 atoms<br> 7 MainChain+H : 2675 atoms<br> 8 SideChain : 5795 atoms<br> 9 SideChain-H : 2078 atoms<br>
10 Prot-Masses : 8470 atoms<br> 11 non-Protein : 54406 atoms<br> 12 Ion : 5 atoms<br> 13 NA : 2 atoms<br> 14 CL : 1 atoms<br> 15 LIG : 53 atoms<br>
16 POPC : 6864 atoms<br> 17 CL- : 2 atoms<br> 18 Other : 6917 atoms<br> 19 NA : 2 atoms<br> 20 CL : 1 atoms<br> 21 LIG : 53 atoms<br>
22 POPC : 6864 atoms<br> 23 CL- : 2 atoms<br> 24 Water : 47484 atoms<br> 25 SOL : 47484 atoms<br> 26 non-Water : 15392 atoms<br> 27 Water_and_ions : 47489 atoms<br>
<br> nr : group ! 'name' nr name 'splitch' nr Enter: list groups<br> 'a': atom & 'del' nr 'splitres' nr 'l': list residues<br> 't': atom type | 'keep' nr 'splitat' nr 'h': help<br>
'r': residue 'res' nr 'chain' char<br> "name": group 'case': case sensitive 'q': save and quit<br> 'ri': residue index<br><b><br>
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<br><br></b>> r15<br><br><br> 28 r_15 : 12 atoms<b><br><br><br>
> <br><br><br> 0 System : 62876 atoms<br> 1 Protein : 8470 atoms<br> 2 Protein-H : 4235 atoms<br> 3 C-alpha : 539 atoms<br> 4 Backbone : 1617 atoms<br>
5 MainChain : 2157 atoms<br> 6 MainChain+Cb : 2652 atoms<br> 7 MainChain+H : 2675 atoms<br> 8 SideChain : 5795 atoms<br> 9 SideChain-H : 2078 atoms<br> 10 Prot-Masses : 8470 atoms<br>
11 non-Protein : 54406 atoms<br> 12 Ion : 5 atoms<br> 13 NA : 2 atoms<br> 14 CL : 1 atoms<br> 15 LIG : 53 atoms<br> 16 POPC : 6864 atoms<br>
17 CL- : 2 atoms<br> 18 Other : 6917 atoms<br> 19 NA : 2 atoms<br> 20 CL : 1 atoms<br> 21 LIG : 53 atoms<br> 22 POPC : 6864 atoms<br>
23 CL- : 2 atoms<br> 24 Water : 47484 atoms<br> 25 SOL : 47484 atoms<br> 26 non-Water : 15392 atoms<br> 27 Water_and_ions : 47489 atoms<br> 28 r_15 : 12 atoms<br>
<br>then</b><b>, i save it with q command<br><br></b>> q<br><br><br>Back Off! I just backed up output.ndx to ./#output.ndx.15#<br><br>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.<br>
<br>Please let know your suggestions to overcome this error.<br><br><br>Thanks,<br><br>ram<br><br><br><b><br><br></b>