oh I should clarify that in 99sb the torsions do not penalize per se -
for a single amino acids you'll get the mirror image energy surface
as compared to L.
On Tue, Sep 9, 2008 at 8:26 PM, Carlos Simmerling
<carlos.simmerling.gmail.com> wrote:
> we carefully checked ff99SB to make sure that D amino acids had the
> right behavior.
> all you have to do is read a pdb with D coords, or if you don't have
> one then we often swap the HA and CB, heavily restrain all but the
> side chain and minimize. for chiral side chains (Thr, Ile, etc) check
> them carefully when you're done.
> carlos
>
>
> On Tue, Sep 9, 2008 at 8:06 PM, David Watson <dewatson.olemiss.edu> wrote:
>> Is it safe to generate sequences in xleap (say with ff03 parameterization)
>> and "flip chirality" on the alpha-carbon to generate the D-amino acid?
>> When I "desc myunit" I see that the residue name is unchanged.
>> I suppose what I am getting at is whether or not the dihedral force
>> constants are defined in a way so that chirality inversion is penalized
>> instead of promoted with such non-standard "standard" amino-acid residues.
>>
>> Thanks
>>
>>
>> ----
>> David Watson • Graduate Student • Medicinal Chemistry • 425 Faser Hall •
>> University MS 38677 • 1.662.915.1663
>>
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>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling.gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
>
--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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Received on Wed Sep 10 2008 - 06:07:52 PDT
