AMBER Archive (2008)

Subject: Re: AMBER: Preparing peptides with D-amino acids

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Sep 09 2008 - 20:14:34 CDT

ok- I have not tried xleap's flip, but examining the structure
visually afterward should let you know, the CORN rule always rules...
from an energy point of view 99sb is fine- maybe someone else has
worked through the details with ff03.

On Tue, Sep 9, 2008 at 9:04 PM, David Watson <dewatson_at_olemiss.edu> wrote:
> On Sep 9, 2008, at 7:28 PM, Carlos Simmerling wrote:
>
>> 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.
>
> For the record, I am not reading coordinates from an external pdb, I am
> building units from scratch in xleap.
> Should I assume that this is also true of peptides built in xleap, with
> chiral inversion either prior- or subsequent-to addition of residues?
>
> I simply select the alpha carbon and "Edit->Flip chirality" so I wouldn't
> imagine that xleap would also flip the topicity of the side chains, but I
> guess that the black-box warning can't be ignored, in any case.
>
> I intend to do requisite minimization after saving the parameter topology
> and input coordinate files.
>
>>
>>
>> On Tue, Sep 9, 2008 at 8:26 PM, Carlos Simmerling
>> <carlos.simmerling_at_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_at_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
>>>>
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-- 
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Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
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Stony Brook University E-mail: carlos.simmerling_at_gmail.com
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