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

[Liu Shiyong]

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'  "?



On Fri, Jan 16, 2009 at 9:19 PM, Mark Abraham <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 (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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