AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Feb 05 2009 - 09:10:18 CST

right. while testing ff99SB, we explicitly looked at D amino acids to
ensure that they produced a free energy map symmetric to the L
version, and they did (but not all parameter sets did this correctly,
depending on phases etc of the various terms)

On Thu, Feb 5, 2009 at 10:02 AM, Andrew Purkiss-Trew
<a.purkiss_at_mail.cryst.bbk.ac.uk> wrote:
> 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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