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>> 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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
