[gmx-users] DNA problem

Mark Abraham Mark.Abraham at anu.edu.au
Sat Aug 22 13:18:56 CEST 2009

mojdeh akhavan wrote:
> Hi
> I have PDB file of DNA (PDB ID: 1D49). I intend generate topology file by
> pdb2gmx. One error is created: (atom O5 in residue DCYT 1 not found in rtp
> entry with 21 atom while sorting atom).
> 2 notes:
> 1: I checked rtp file for used force field. In rtp file, there is [DCYT] ,
> [DTYM] , [DADE] and [DGUA].
> 2: I checked PDB file. residue DCYT 1 has only 16 atoms.

You need to provide a lot more information about what you're doing - 
GROMACS version and which force field, for starters. When reporting a 
problem, copy and paste the exact error, don't filter it through your 
brain and fingers :-)


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