[gmx-users] pdb2gmx and protein DNA complexes

Erik Marklund erikm at xray.bmc.uu.se
Wed Nov 8 18:44:24 CET 2006

Yes, very recently actually. What forcefield are you using? If you're using the AMBERXX-port, you might want to have a look at http://folding.stanford.edu/ffamber/. 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.

  ----- Original Message ----- 
  From: Debojyoti Dutta 
  To: gmx-users at gromacs.org 
  Sent: Wednesday, November 08, 2006 6:08 PM
  Subject: [gmx-users] pdb2gmx and protein DNA complexes


  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.

  Program pdb2gmx, VERSION 3.3
  Source code file: resall.c, line: 438 

  Fatal error:
  Residue 'C' not found in residue topology database

  The pdb segment is as follows:

  ATOM   1239  NZ  LYS B 513     -24.159  16.372 -25.774  1.00 51.42           N
  ATOM   1249  N1    C C   1     - 10.253   8.018  40.704  1.00 25.86           N

  Has anyone encountered this problem before?


  Debojyoti Dutta, PhD (USC)


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