[gmx-users] dna with charmm36

Justin Lemkul jalemkul at vt.edu
Wed Feb 5 16:15:18 CET 2014

On 2/5/14, 9:49 AM, gromacs query wrote:
> Hi All
> I have simple DNA pdb which has just 5 DA residues built from NAB in AMBER.
> I am trying to use pdb2gmx with charmm36-jan2014.ff downloaded from:
>   http://mackerell.umaryland.edu/CHARMM_ff_params.html
> pdb2gmx -f a.pdb -o gro.pdb -ff charmm36-jan2014
> I have changed all names according to DA residue defined in
> charmm36-jan2014.ff/merged.rtp but still I get error:
> Fatal error:
> atom N not found in buiding block 1DA while combining tdb and rtp

Use -ter to specify the appropriate termini.  An unfortunate consequence of our 
approach is that the protein and DNA termini are in one file.  We are looking at 
implementing a more generalized solution, but it won't be for a while that we 
actually get to it.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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