Hi I have checked the manual, but it did not help. Checking the cgnr column did not help either. 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? On Mon, Jan 19, 2009 at 11:59 AM, Justin A. Lemkul <[email protected]> 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 >> <[email protected]<mailto: >> [email protected]>> 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 [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> 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: [email protected] <mailto:[email protected]> ([email protected] <mailto: >> [email protected]> or [email protected] <mailto:[email protected]>) >> Homepage: http://www.people.ku.edu/~syliu<http://www.people.ku.edu/%7Esyliu> >> Lab: http://vakser.bioinformatics.ku.edu/people >> Phone: (785) 864-1962 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [email protected]. >> 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 [email protected] > 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 [email protected]. > 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: [email protected] ([email protected] or [email protected]) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962
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