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

[Liu Shiyong]

Thanks.

I used the PDB file with H .  It works though it's still a mystery for me
why PDB file without H couldn't work.



On Tue, Jan 20, 2009 at 1:53 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
>
> --
> ========================================
>
> 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
>
> ========================================
>



-- 
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab:    http://vakser.bioinformatics.ku.edu/people
Phone:      (785) 864-1962
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