[gmx-users] Mn/Mn2+ Parameters included in Amberff

[Justin Lemkul]

On 6/26/16 4:05 PM, Vito Spadavecchio wrote:
> Hello
>
> It looks like parameters for Mn/Mn2+ were (somewhat) recently developed for
> Amber forcefield (http://pubs.acs.org/doi/abs/10.1021/ct400055v); I'd like
> to use these parameters for a simulation I'd like to run on MntR (PDB: 1ON2
> <http://www.rcsb.org/pdb/explore.do?structureId=1on2>), but can't seem to
> find these files anywhere. Does anyone know where to get them, or how to
> extract them from Amber (I got ambertools16 but can't seem to find them
> there either). Any help is greatly appreciated!
>

It looks like you'll have to introduce new residues with the parameters 
specified in the paper.  If they're not already available in some convenient 
format, open Chapters 4 and 5 of the GROMACS manual and fire up your favorite 
text editor.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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