[gmx-users] pdb2gmx with DNA

[Justin A. Lemkul]

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?

-Justin

> Thanks a lot
> 
> George-- 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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