[gmx-users] make index

[Justin Lemkul]

On 7/23/18 8:42 AM, farial tavakoli wrote:
> 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

You need to use an input file format that includes chain information, 
like .pdb or .tpr - there is no chain information in a .gro file.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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