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

Justin Lemkul jalemkul at vt.edu
Mon Jun 27 14:53:22 CEST 2016



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
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University of Maryland, Baltimore
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Baltimore, MD 21201

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