[gmx-users] About RNA simulation

Justin Lemkul jalemkul at vt.edu
Thu Mar 24 14:23:22 CET 2016

On 3/24/16 8:44 AM, 柳青 wrote:
> hello, everyone,
>         I wanted to simulate a dsRNA(PDB ID:2MVY) by using gromos53a6, but  failed at pdb2gmx. The error information said:
>                     Fatal error:
>                     atom N not found in buiding block 1GUA while combining tdb and rtp
>                     For more information and tips for troubleshooting, please check the GROMACS
>         I had made the nucleotide name agree with the rtp file. Can you help me?Thank you.

The GROMOS force fields include parameters for nucleotides (and are weirdly 
listed in aminoacids.rtp) but they do not appear to have any ability to assign 
5' and 3' termini (as there are only protein termini listed in the .tdb files). 
  Use a better force field like CHARMM36.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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