[gmx-users] Amber03ws includes an unexpected dihedral with atoms -C N CA CB

Justin Lemkul jalemkul at vt.edu
Wed May 17 13:33:54 CEST 2017

On 5/17/17 6:04 AM, Ramon Crehuet wrote:
> Dear all,
> I would like to use the Amber03ws force field described in Best, Zheng and Mittal, J. Chem. Theor. Comput., 10, 5113-5124, 2014.
> This force field is contributed in http://www.gromacs.org/Downloads/User_contributions/Force_fields
> When using it, Gromacs reports a warning about a CB atom in GLY residues. I could trace it to the aminoacids.rtp file, which contains these lines for the GLY residue:
> [ dihedrals ]
> CA C +N +H
> O C +N +H
> -C N CA CB
> -C N CA C
> CA C +N +CA
> O C +N +CA
> -C N CA HA1
> -C N CA HA2
> HA1 CA C +N
> HA2 CA C +N
> The presence of the CB atom is an error? Can I simply ignore this warining?

Probably better to fix the file, but it shouldn't do any actual harm.  This 
problem was propagated from older Amber force field files that I fixed a long 
time ago.



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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