AMBER Archive (2009)

Subject: Re: [AMBER] parameter files for D-amino acid

From: Andrew Purkiss-Trew (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Thu Feb 05 2009 - 09:02:25 CST

This should be no need for additional parameters, as there is no chiral
term in ff99sb. In other words, the force field as it is will describe
both L and D amino acids. Indeed, you will sometimes see L -> D flipping
if you run at high temperatures during a simulation.

Therefore, you can just load your protein with a D amino acid and leap
will correctly parameterise it with ff99sb.

Quantum mechanically, there are likely to be slight differences in the
energies between L and D, but this will be very small compared to the
other inaccuracies in a macromolecular forcefield.

Hope this helps

On Thu, 2009-02-05 at 20:19 +0530, vijayaraj_at_clri.res.in wrote:
> There are some discussions in this forum regarding the D amino acid
> incorporation into the protein. But there is no clear definition for
> setting up parameters in ff99sb. Can someone give suggestion on this
> regard?
>
>
> > D amino acids have been tested to work properly with ff99SB, not sure
> > about other parameter sets.
> >
> >
> >
> >
> > On Thu, Feb 5, 2009 at 8:04 AM, Vsatheesh Patil
> > <vsatheeshpatil_at_yahoo.com> wrote:
> >> Dear all,
> >> I want to know how to create the parameter file for D-amino
> >> acid as i am working on the L and D amino acid.
> >>
> >>
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