Hi<br>I have checked the manual, but it did not help. Checking the cgnr column did not help either.<br>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. <br>
As the result, I am getting "1996 and 1998 are in different energy groups".<br><br>ATOM 1996 O ASN B 248 49.634 9.874 85.195 1.00 0.00<br>ATOM 1997 OXT ASN B 248 50.217 10.536 83.158 1.00 0.00<br>
TER<br>ATOM 1998 N GLY C 249 70.273 30.186 73.098 1.00 0.00<br>ATOM 1999 CA GLY C 249 68.973 30.327 72.421 1.00 0.00<br><br> As you see, atoms 1996 and 1998 should be in different groups. I have no any idea whether <br>
it's related to Gromacs or to the pdb file, or to something else? Could anybody advice SOMETHING? <br>
<br><br><br><div class="gmail_quote">On Mon, Jan 19, 2009 at 11:59 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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><div></div><div class="Wj3C7c"><br>
<br>
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;">
<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>
</blockquote>
<br></div></div>
The manual has information about charge groups. To see exactly what you've split apart, check your topology (cgnr column).<br>
<br>
-Justin<br>
<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">
<br>
<br>
On Fri, Jan 16, 2009 at 9:19 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br>
Liu Shiyong wrote:<br>
<br>
Hi,<br>
<br>
We have a protein with two chains A and B. We want to calculate<br>
the interaction energy only.<br>
Would you advise how to define the energy groups for the chains<br>
and how to output the interaction<br>
energy between chains A and B ?<br>
<br>
<br>
Have a search of the mailing list archives, similar questions have<br>
been dealt with there. Also look in the manual for energy groups in<br>
several places.<br>
<br>
Mark<br>
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<br>
-- <br>
Shiyong Liu<br>
Postdoc<br>
center for bioinformatics in the university of kansas<br>
Lab: (785)864-1962<br></div>
Email: <a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a> <mailto:<a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a>> (<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a> <mailto:<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a>> or <a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a> <mailto:<a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a>>)<div class="Ih2E3d">
<br>
Homepage: <a href="http://www.people.ku.edu/%7Esyliu" target="_blank">http://www.people.ku.edu/~syliu</a><br>
Lab: <a href="http://vakser.bioinformatics.ku.edu/people" target="_blank">http://vakser.bioinformatics.ku.edu/people</a><br>
Phone: (785) 864-1962<br>
<br>
<br></div>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</div></div></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>