My feeling is that preparing just separate prepfiles
for D-AA's with with the same charges as for L-AA's would allow for
mixing those tow things together and is a very good approximation.
Piotr
On Wed, 21 Sep 2005, justin litchfield wrote:
> Date: Wed, 21 Sep 2005 00:50:36 -0700
> From: justin litchfield <litch.stanford.edu>
> Reply-To: amber.scripps.edu
> To: amber.scripps.edu
> Subject: Re: AMBER: D-enantiomers
>
> I agree in that this was my initial concern: that they are diastereomers once
> you put the D-AA in with L-AA's. but as far as I know, these force fields
> are basically built on a unit-by-unit basis - with the units being the amino
> acids - and if that were not the case, you would need one Ser force field
> that was for say xxx-Ser-Glu-xxx and one that was for xxx-Ser-Lys-xxx. this
> is obviously not the case so one must assume that the force fields are for
> each individual unit in isolation. so though I cannot speak to this concern
> specifically as it concerns the model, chemically I think that it is sensible
> to use the same parameters for both D- or L- amino acids. hope that makes
> sense,
>
> justin
>
>
> On Sep 20, 2005, at 11:53 PM, FyD wrote:
>
>> Quoting "Thomas E. Cheatham, III" <cheatham.chpc.utah.edu>:
>>
>>
>>>> I am relatively new to Amber, but have not found any information on the
>>>> following topic. Is there an easy way to implement the D amino acids in
>>>> Amber? I am looking to simulate a short peptide which contains one or
>>>> more
>>>> D-enantiomers along the backbone.
>>>>
>>>
>>> As enantiomers have equivalent properties (outside of a chiral environment
>>> other than bending plane polarized light), one would not expect that the
>>> charges or intra-molecular parameters would be different for D vs. L in an
>>> empirical force field.
>>>
>>
>> And what about introducing a D amino-acid (AA) in a sequence composed of L
>> AA ?
>> Each AA (D or L enantiomer), individually I mean, is optically equivalent,
>> but a
>> di-AA D-L compared to L-L are diastereoisomers. In this case, (compared to
>> the
>> "ALL" L sequence), I guess, you can expect charge differences (consequently
>> FF
>> param. differences).
>> Since the charges are derived for each "UNIT" individually (L enantiomers),
>> the
>> problem could arise from mixing them which can lead to diateroeisomers. Am
>> I
>> wrong or is it simply "too much" for an empirical force field ?
>>
>> Regards, Francois
>>
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Received on Wed Sep 21 2005 - 09:53:00 PDT
