Dear Professor David A. Case,
As mentioned in Junmei Wang's paper on JACS(2001) , they solve such problem by doing normal mode
analysis on redisues 12 angstron around the center of the ligand .
I don't know how they operate it in detail .
Do they just cut the hole protein to small pieces ,and then do the normal mode analysis ?
Or is there one way in the Nmode module of Amber can do the normal mode analysis on special groups ,just partial vibrational mode of the molecule was analyzed ?
Thank you very much for your sincerely help .!
Yours Sincerely,
Changge Ji
======= 2006-08-29 13:55:53 您在来信中写道：=======
>On Tue, Aug 29, 2006, AYTUG TUNCEL wrote:
>>
>> I am trying to do nmode calculation of mm_pbsa method using amber8. My
>> protein is dimeric composed of totally 13776 atoms (both chains have nearly
>> equal length). I am wondering about the maximum number of atoms that nmode
>> can be applied. As far as I found in the archive it is about 8000 atoms. If
>> this is the case how can I apply the method to my system, is there any
>> trick about changing a parameter? thanks in advance...
>
>This size would require a *lot* of patience and computer memory, and is
>probably not realistically feasible with Amber's nmode program.
>
>You might consider looking at NAB:
>
> http://www3.interscience.wiley.com/cgi-bin/abstract/112750181/ABSTRACT
> http://www.scripps.edu/case
>
>But this is a real daunting project. You might really want to consider other
>methods of estimating entropies, (or even of investigating protein-protein
>interactions, depending on what your goals are.)
>
>...dac
>
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致
礼！
Changge Ji
jcg.itcc.nju.edu.cn
2006-08-29
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Received on Wed Aug 30 2006 - 06:07:14 PDT
