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

Liu Shiyong liushiyong at gmail.com
Tue Jan 20 18:41:56 CET 2009 

Hi
I have checked the manual, but it did not help. Checking the cgnr column did
not help either.
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?



On Mon, Jan 19, 2009 at 11:59 AM, Justin A. Lemkul <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>> 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> (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<http://www.people.ku.edu/%7Esyliu>
>> Lab:    http://vakser.bioinformatics.ku.edu/people
>> Phone:      (785) 864-1962
>>
>>
>> ------------------------------------------------------------------------
>>
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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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-- 
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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