[gmx-users] pdb2gmx fatal error

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 26 21:15:35 CEST 2009

Dave Hassan wrote:
> Hi,
> I'm trying to run a simple simulation of a DNA hairpin pdb entry 1pqt.
> When I run pdb2gmx  with the G43a1 force field I get the error:
> Warning: 'DG' not found in residue topology database, trying to use 'DGUA'
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.5
> Source code file: pdb2gmx.c, line: 429
> Fatal error:
> Atom O5' in residue DGUA 1 not found in rtp entry with 25 atoms
>              while sorting atoms
> -------------------------------------------------------
> any hints?

Atom naming in the coordinate file must match what is expected in the .rtp file. 
  Check out the .rtp file and adjust the coordinate file as necessary.  With 
nucleic acids, it's usually a difference between ' and * in the sugar.


> Thanks,
> Dave Hassan
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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