[gmx-users] make_ndx unable to save

[Justin A. Lemkul]

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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