AMBER Archive (2006)

Subject: Re: Re: AMBER: nmode: number of atoms limitation

From: Changge Ji (
Date: Tue Aug 29 2006 - 01:33:27 CDT

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 艇壓栖佚嶄亟祇=======

>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:
>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.)
>The AMBER Mail Reflector
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= = = = = = = = = = = = = = = = = = = =


        Changge Ji

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