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<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>
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<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>
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