<br>Hi,<br><br> I searched the mail list. <br> I found a solution to define energy groups by chain.<br><br>make_ndx -f ${df}.pdb -o ${file}.ndx > ${file}.output.make_ndx << _EOF_<br>del 0-9<br>chain A and B<br>chain C<br>
q<br>_EOF_<br><br>But , I run<br>grompp -maxwarn 10 -f em.mdp -c ${file}.gro -n ${file}.ndx -p ${file}.top -po ${file}.mdout.mdp -o${file}.input.tpr <br><br>and got error information:<br><br>-------------------------------------------------------<br>
Program grompp, VERSION 4.0.2<br>Source code file: grompp.c, line: 150<br><br>Fatal error:<br>atoms 1996 and 1998 in charge group 296 of molecule type 'Protein_B' are in different energy groups<br>-------------------------------------------------------<br>
<br>I checked my *.ndx file:<br><br>1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995<br>1996 1997<br>[ chC ]<br>1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012<br>2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027<br>
<br><br> 1996 and 1998 are in different energy groups.<br><br>What is the meaning of " the charge group 296 of molecule type 'Protein_B' "?<br><br><br><br><div class="gmail_quote">On Fri, Jan 16, 2009 at 9:19 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">Liu Shiyong wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
We have a protein with two chains A and B. We want to calculate the interaction energy only.<br>
Would you advise how to define the energy groups for the chains and how to output the interaction<br>
energy between chains A and B ?<br>
</blockquote>
<br></div>
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.<br>
<br>
Mark<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote></div><br><br clear="all"><br>-- <br>Shiyong Liu<br>Postdoc<br>center for bioinformatics in the university of kansas<br>Lab: (785)864-1962<br>Email: <a href="mailto:syliu@ku.edu">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/~syliu">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people">http://vakser.bioinformatics.ku.edu/people</a><br>Phone: (785) 864-1962<br>