ram bio wrote:
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.
You need to provide your custom index group as input to make_ndx if you want to
make use of that group further, e.g.:
make_ndx -f jhcdyprod31ns.gro -n output.ndx -o output2.ndx
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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