[gmx-users] pdb2gmx error

Justin Lemkul jalemkul at vt.edu
Mon Jul 27 02:19:01 CEST 2015

On 7/26/15 6:46 AM, faride badalkhani wrote:
> Dear all,
> could anybody help me at this error?
> Fatal error:
> atom N not found in buiding block 1AMC while combining tdb and rtp
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors

Use -ter and select appropriately (probably "None" in the case of a polymer, 
provided you're following 
http://www.gromacs.org/Documentation/How-tos/Polymers).  If you don't specify 
terminal patching, pdb2gmx defaults to assuming you want protein-like N- and 
C-terminal termini.



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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