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

[Justin A. Lemkul]

Liu Shiyong wrote:
> 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.
>  

Because the atoms will be numbered wrong.  When you use pdb2gmx, hydrogens will 
be added to some groups (polar groups, aromatics, N-termini, etc).  So, starting 
with chain A, which now has three additional protons on the N, the numbering 
will be very different from the original pdb file.  Check out each .pdb file and 
your topologies and see for yourself how quickly the numbering differs.

-Justin

> 
> 
> On Tue, Jan 20, 2009 at 1:53 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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 <http://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 <mailto:syliu at ku.edu> (shiyongliu at ku.edu 
> <mailto:shiyongliu at ku.edu> or liushiyong at ku.edu <mailto:liushiyong at ku.edu>)
> Homepage: http://www.people.ku.edu/~syliu
> Lab:    http://vakser.bioinformatics.ku.edu/people
> Phone:      (785) 864-1962

-- 
========================================

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

========================================