AMBER Archive (2008)

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

From: David Watson (dewatson_at_olemiss.edu)
Date: Tue Sep 09 2008 - 20:04:44 CDT

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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