[gmx-users] pdb2gmx with DNA

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 10 02:08:25 CEST 2010

Patargias, George wrote:
> Thanks for your reply Justin. 
> I am trying to generate a topology dor a dna structure using the charmm dna.rtp 
> I have renamed the residue name to DA , DG etc. I have also set DA5 and DC3 for 
> the 5' and 3' ends
> I got this error 
> Fatal error:
> atom N not found in buiding block 2DG while combining tdb and rtp
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> I quess I need to change something in the .rtp and/or the .tdb files. But what?

Maybe, maybe not.  It looks like pdb2gmx is trying to treat your DNA as protein. 
  What is your command line?  What are you choosing for termini?


> Thanks a lot
> George-- 
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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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