[gmx-users] Phosphohistidine parameters

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 7 12:18:50 CET 2008

Check the Users' Contributions site.  I believe there are some utilities for
converting between AMBER and GROMACS formats.


Quoting Eddie Mende <pckboy at gmail.com>:

> Hello
> I just found a page with amber forcefield parameters for phosphohistidine
> however these are to be used by the AMBER program
> Is it easy (or is there any util) that I can use to translate parameters
> form one
> format into another?.
> Eduardo
> Justin A. Lemkul wrote:
> > Eduardo,
> >
> > To my knowledge, no parameters exist for phosphorylated histidine.  You
> will
> > have to derive them in a manner consistent with the original forcefield.
> If
> > you are interested in breaking the His-PO3 bond, you will need to do some
> > fairly rigorous QM/MM, for which an all-atom force field is the only way to
> go
> > (Amber or OPLSAA).  Sorry to say, I do not have parameters available for
> either
> > of these force fields that include your phosphorylated species.
> >
> > -Justin
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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