<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
<META content="MSHTML 6.00.2900.2963" name=GENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=#ffffff>
<DIV><FONT face=Arial size=2>...and not just the atoms. Make sure that the
residue names are the correct ones for your forcefield. Apparently, the
forcefield you're using does not have a 'C'-residue.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>/Erik</FONT></DIV>
<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=erikm@xray.bmc.uu.se href="mailto:erikm@xray.bmc.uu.se">Erik
Marklund</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Wednesday, November 08, 2006 6:44
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [gmx-users] pdb2gmx and
protein DNA complexes</DIV>
<DIV><FONT face=Arial size=2></FONT><FONT face=Arial size=2></FONT><BR></DIV>
<DIV><FONT face=Arial size=2>Yes, very recently actually. What forcefield are
you using? If you're using the AMBERXX-port, you might want to have a look at
<A
href="http://folding.stanford.edu/ffamber/">http://folding.stanford.edu/ffamber/</A>.</FONT><FONT
face=Arial size=2> Regardless of your ff, make sure that the atoms in
your pdb match the ones in ff[your_forcefield].rtp. Oh, and read the
manual.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>/Erik</FONT></DIV>
<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=ddutta@usc.edu href="mailto:ddutta@usc.edu">Debojyoti Dutta</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Wednesday, November 08, 2006 6:08
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] pdb2gmx and
protein DNA complexes</DIV>
<DIV><BR></DIV>Hi <BR><BR>I am trying to simulate a protein DNA complex but
I am stuck at the pdb2gmx stage as it gets stuck when it encounters a
nucleotide.<BR><BR clear=all>Program pdb2gmx, VERSION 3.3<BR>Source code
file: resall.c, line: 438 <BR><BR>Fatal error:<BR>Residue 'C' not found in
residue topology database<BR><BR>The pdb segment is as
follows:<BR><BR>ATOM 1239 NZ LYS B
513 -24.159 16.372 -25.774 1.00
51.42
N<BR>ATOM 1249 N1 C C
1 - 10.253 8.018 40.704 1.00
25.86
N<BR><BR>Has anyone encountered this problem
before?<BR><BR>Regards<BR>Debo<BR><BR>--
<BR>---------------------------------------------<BR>Debojyoti Dutta, PhD
(USC)<BR><A
href="http://catarina.usc.edu/~ddutta">http://catarina.usc.edu/~ddutta</A> <BR>---------------------------------------------<BR>
<P>
<HR>
<P></P>_______________________________________________<BR>gmx-users mailing
list
gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please
don't post (un)subscribe requests to the list. Use the <BR>www interface or
send it to gmx-users-request@gromacs.org.<BR>Can't post? Read
http://www.gromacs.org/mailing_lists/users.php</BLOCKQUOTE>
<P>
<HR>
<P></P>_______________________________________________<BR>gmx-users mailing
list
gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please
don't post (un)subscribe requests to the list. Use the <BR>www interface or
send it to gmx-users-request@gromacs.org.<BR>Can't post? Read
http://www.gromacs.org/mailing_lists/users.php</BLOCKQUOTE></BODY></HTML>