AMBER Archive (2005)

Subject: Re: AMBER: D-enantiomers

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Sep 22 2005 - 06:35:06 CDT

We recently published a paper in JMB where we used Amber
with mixed D and L amino acids.We confirmed that the force field indeed
was symmetric and everything worked fine. We also routinely
use dihedral restraints to maintain chirality in high temperature MD
such as REMD. It can flip if you go high enough.
Worrying about L- and D- combinations is at the level of
polarizability.

carlos

> On Wed, 21 Sep 2005, justin litchfield wrote:
>
>> Date: Wed, 21 Sep 2005 00:50:36 -0700
>> From: justin litchfield <litch_at_stanford.edu>
>> Reply-To: amber_at_scripps.edu
>> To: amber_at_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_at_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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