[gmx-users] pdb2gmx with DNA

Patargias, George patargias at usf.edu
Sat Jul 10 01:51:17 CEST 2010

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?

Thanks a lot


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