[gmx-users] pdb2gmx and protein DNA complexes

[Erik Marklund]

...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.

/Erik
  ----- Original Message ----- 
  From: Erik Marklund 
  To: Discussion list for GROMACS users 
  Sent: Wednesday, November 08, 2006 6:44 PM
  Subject: Re: [gmx-users] pdb2gmx and protein DNA complexes


  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.

  /Erik
    ----- 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


    Hi 

    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?

    Regards
    Debo

    -- 
    ---------------------------------------------
    Debojyoti Dutta, PhD (USC)
    http://catarina.usc.edu/~ddutta        
    ---------------------------------------------



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