[gmx-users] Qestion about how to define groups by chain id in a protein ?

[Justin A. Lemkul]

Liu Shiyong wrote:

<snip>

The problem lies here:

Including chain 1 in system: 1296 atoms 125 residues
Including chain 2 in system: 1274 atoms 123 residues
Including chain 3 in system: 2085 atoms 201 residues

This suggests that chain 2 (Protein B) should contain numbers up to about 2500.

>         ATOM   1996  O   ASN B 248      49.634   9.874  85.195  1.00  0.00
>         ATOM   1997  OXT ASN B 248      50.217  10.536  83.158  1.00  0.00
>         TER
>         ATOM   1998  N   GLY C 249      70.273  30.186  73.098  1.00  0.00
>         ATOM   1999  CA  GLY C 249      68.973  30.327  72.421  1.00  0.00
> 

This is the original .pdb file, then?  The hydrogens will be missing from the 
appropriate groups in the pdb2gmx-processed output structures.  You can check 
the numbering (and pertinent charge groups) in the topology for each chain, to 
be sure.

>                make_ndx -f ${df}.pdb  -o ${file}.ndx >
>         ${file}.output.make_ndx
>                << _EOF_
>                del 0-9
>                chain A and B
>                chain C
>                q
>                _EOF_

This should work, with the right input :)

-Justin

-- 
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Justin A. Lemkul
Graduate Research Assistant
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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