Re: [AMBER] General question

From: Gould, Ian R <i.gould.imperial.ac.uk>
Date: Tue, 14 Aug 2012 08:06:37 +0000

Hi George,

You may also wish to take a look at a paper of ours were we tried to
address some of these issues
Bradshaw RT, Patel BH, Tate EW, et al <>, Comparing experimental and
computational alanine scanning techniques
for probing a prototypical protein-protein interaction., Protein Eng Des
Sel, 2011, Vol:24, Pages:197-20

doi:10.1093/protein/gzq047

Cheers
Ian


Women love us for our defects. If we have enough of them, they will
forgive us everything, even our intellects.
Oscar Wilde, 
-- 
Dr Ian R Gould
Reader in Computational Chemical Biology
Department of Chemistry
Imperial College London
Exhibition Road
London
SW7 2AY
E-mail i.gould.imperial.ac.uk
http://www3.imperial.ac.uk/people/i.gould
Tel +44 (0)207 594 5809
On 14/08/2012 03:08, "Jason Swails" <jason.swails.gmail.com> wrote:
>On Mon, Aug 13, 2012 at 4:42 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Hi everybody,
>>
>> I know that there is no prescribed answer to my question but I'd still
>> like to ask as my computational power is rather limited (running a 24
>>core
>> Mac)
>>
>> In calculating free energies of binding (MMPBSA) is it preferable to
>>run a
>> long trajectory or several smaller ones? I'm dealing with a proteins of
>> ~150 residues.
>>
>
>Genheden et. al has discussed this point (DOI 10.1002/jcc.21366) and come
>to the conclusion that several short simulations give rise to more
>statistically converged answers, since you obtain more uncorrelated
>structures that way.
>
>Of course if you started with the same structure and ran only 10 fs, you
>would get statistically converged answers as well (in that the standard
>deviation would be small), since they're all effectively the same
>structure
>(and you never know, the various snapshots may even appear uncorrelated :)
>).  That's obviously not what they did there (they ran ~200 ps per
>simulation, IIRC), but I'm still not entirely convinced.
>
>HTH,
>Jason
>
>
>> Your experience is valued
>>
>> George
>>
>>
>>
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>>
>
>
>
>-- 
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>352-392-4032
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Received on Tue Aug 14 2012 - 01:30:03 PDT
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