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

[Justin A. Lemkul]

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
> 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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