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 <jalem...@vt.edu
<mailto:jalem...@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.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@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: sy...@ku.edu <mailto:sy...@ku.edu> <mailto:sy...@ku.edu
<mailto:sy...@ku.edu>> (shiyong...@ku.edu
<mailto:shiyong...@ku.edu> <mailto:shiyong...@ku.edu
<mailto:shiyong...@ku.edu>> or liushiy...@ku.edu
<mailto:liushiy...@ku.edu> <mailto:liushiy...@ku.edu
<mailto:liushiy...@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 <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: sy...@ku.edu <mailto:sy...@ku.edu> (shiyong...@ku.edu
<mailto:shiyong...@ku.edu> or liushiy...@ku.edu <mailto:liushiy...@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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