[gmx-users] Re: pdb2gmx problem

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 22 13:47:56 CEST 2009

leila karami 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.
> pleas guide me

Please keep all Gromacs-related correspondence on the gmx-users list.

An identical question was just posted by someone else, and an answer given.  If 
your structure has missing atoms, they must be modeled back in with some other 



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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