On Jun 24, 2011, at 2:56 PM, Balazs Jojart <jojartb.gmail.com> wrote:
> Dear Dr. Case,
> If we use quasi-harmonic approximations instead of normal mode analysis,
> then the decomposition is possible. Or not?
> Balazs
The same thing that applies to the normal mode calculation that Dave pointed out, that the eigenvectors of the lowest eigenvalues (frequencies) are global motions delocalized over many residues, also applies to the covariance matrix used in the quasi-harmonic approximation.
That said, I *think* some decomposition scheme for entropy was added to nmode (not in NAB, so it will be vacuum only) that can be used in mm_pbsa.pl. It may only have been for amber 11... Check the manual for details (and references for how they project the normal mode contributions onto each residue to assess its validity)
HTH,
Jason
>
> The calculations appli
>
> On 06/24/2011 07:43 PM, Daniel Aiello wrote:
>> Thanks.
>> On Jun 24, 2011, at 11:57 AM, David A. Case wrote:
>>
>>> On Fri, Jun 24, 2011, Daniel Aiello wrote:
>>>
>>>> Does Amber10 have a built in method for decomposing entropic components
>>>> on a per residue or pair-wise residue basis? Thanks,
>>> No. For biomolecules, the main contributions to entropy come from
>>> low-frequency, collective motions that are not associated with any particular
>>> residue.
>>>
>>> ....dac
>>>
>>>
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>
>
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> Balazs Jojart, Ph.D.
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Received on Fri Jun 24 2011 - 14:30:06 PDT
