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

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 20 19:07:54 CET 2009 


Liu Shiyong wrote:
> Hi
> I have checked the manual, but it did not help. Checking the cgnr column 
> did not help either.

Well, did it indicate that these atoms are indeed in the same charge group?  I 
suggested before that you check out your topology to see how grompp is 
interpreting it.  If, as you say, these chains should be separate, then why is 
grompp thinking they are in a joined molecule?  What command did you give pdb2gmx?

> What I do is just splitting the pdb file into two energy groups (chains 
> A+B and C). I do not change any definitions of charge groups in Gromacs.
> As the result, I am getting "1996 and 1998 are in different energy groups".
> 
> 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
> 
> As you see, atoms 1996 and 1998 should be in different groups. I have no 
> any idea whether
> it's related to Gromacs or to the pdb file, or to something else? Could 
> anybody advice SOMETHING?
> 

Again, check the topology to see what pdb2gmx gave you.  Consider what you did 
at the pdb2gmx step.  Does it help to process each chain separately and, for 
example:

#include "Protein_A.itp"
#include "Protein_B.itp"
#include "Protein_C.itp"

...in the topol.top?

-Justin

> 
> 
> On Mon, Jan 19, 2009 at 11:59 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Liu Shiyong wrote:
> 
> 
>         Hi,
> 
>          I searched the mail list.
>          I found a solution to define energy groups by chain.
> 
>         make_ndx -f ${df}.pdb  -o ${file}.ndx > ${file}.output.make_ndx
>         << _EOF_
>         del 0-9
>         chain A and B
>         chain C
>         q
>         _EOF_
> 
>         But , I run
>         grompp -maxwarn 10 -f em.mdp -c ${file}.gro -n ${file}.ndx -p
>         ${file}.top -po ${file}.mdout.mdp -o${file}.input.tpr
> 
>         and got  error information:
> 
>         -------------------------------------------------------
>         Program grompp, VERSION 4.0.2
>         Source code file: grompp.c, line: 150
> 
>         Fatal error:
>         atoms 1996 and 1998 in charge group 296 of molecule type
>         'Protein_B' are in different energy groups
>         -------------------------------------------------------
> 
>         I checked my *.ndx file:
> 
>         1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993
>         1994 1995
>         1996 1997
>         [ chC ]
>         1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
>         2011 2012
>         2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025
>         2026 2027
> 
> 
>          1996 and 1998 are in different energy groups.
> 
>         What is  the meaning of  " the charge group 296 of molecule type
>         'Protein_B'  "?
> 
> 
>     The manual has information about charge groups.  To see exactly what
>     you've split apart, check your topology (cgnr column).
> 
>     -Justin
> 
> 
> 
>         On Fri, Jan 16, 2009 at 9:19 PM, Mark Abraham
>         <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
>         <mailto:Mark.Abraham at anu.edu.au
>         <mailto:Mark.Abraham at anu.edu.au>>> wrote:
> 
>            Liu Shiyong wrote:
> 
>                Hi,
> 
>                 We have a protein with two chains A and B. We want to
>         calculate
>                the interaction energy only.
>                Would you advise how to define the energy groups for the
>         chains
>                and how to output the interaction
>                energy between chains A and B ?
> 
> 
>            Have a search of the mailing list archives, similar questions
>         have
>            been dealt with there. Also look in the manual for energy
>         groups in
>            several places.
> 
>            Mark
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> 
> 
> 
>         -- 
>         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> <mailto:syliu at ku.edu
>         <mailto:syliu at ku.edu>> (shiyongliu at ku.edu
>         <mailto:shiyongliu at ku.edu> <mailto:shiyongliu at ku.edu
>         <mailto:shiyongliu at ku.edu>> or liushiyong at ku.edu
>         <mailto:liushiyong at ku.edu> <mailto:liushiyong at ku.edu
>         <mailto:liushiyong at ku.edu>>)
> 
>         Homepage: http://www.people.ku.edu/~syliu
>         <http://www.people.ku.edu/%7Esyliu>
>         Lab:    http://vakser.bioinformatics.ku.edu/people
>         Phone:      (785) 864-1962
> 
> 
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> 
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> 
>     -- 
>     ========================================
> 
>     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
> 
>     ========================================
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> 
> 
> 
> -- 
> 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

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