AMBER Archive (2005)

Subject: Re: AMBER: mm_pbsa

From: Ray Luo (rluo_at_uci.edu)
Date: Fri Nov 11 2005 - 17:57:04 CST

Hi Wei,

Could you email me your files so I can take a look why your pbsa output
disagrees with your Delphi output? Please email me the files only for
the snapshot where you see the largest difference.

Best,
Ray

Wei Chen wrote:

>Hi, Ray,
>
>Thank you for your reply!
>
>Did you mean bugfix.49? It supposed to be fix by my administor. But I checked
>the pb_force.f file. It doesn't. I am wondering how I can "temporarily force
>the net charges of neutral systems zero within rounding error". Actually, my
>proteins have a net charge '+1'.
>
>The radii for pb and gb are used as the same as those in the "Example" fold.
>
>Regards,
>
>Wei Chen
>
>
>Quoting Ray Luo <rluo_at_uci.edu>:
>
>
>
>>Did you patch bugfix.48 for pbsa? Are you sure you have used the same
>>radii for pb and gb?
>>
>>Wei Chen wrote:
>>
>>
>>
>>>Hello, all Amber users,
>>>
>>>I am using mm_pbsa in Amber8 to calculate binding free energy of two-protein
>>>binding. When I used PB or GB to calculate polar solvation energy, I got
>>>
>>>
>>very
>>
>>
>>>different values. The free energies (not including entropy) are
>>>
>>>
>>93.28+/-90.46
>>
>>
>>>kcal/mol with PB and -37.43+/-5.54 kcal/mol with GB. First of all, the mean
>>>value with PB is positive, which doesn't make any sense. And the standard
>>>deviation with PB is so large that it is the same order as the mean value.
>>>
>>>
>>The
>>
>>
>>>value with GB seems to be more acceptable. However, I think that GB is an
>>>approximation to PB. So anybody can help me to understand the results?
>>>
>>>Thanks!
>>>
>>>Wei Chen
>>>
>>>--
>>>
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>>>The AMBER Mail Reflector
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>>>.
>>>
>>>
>>>
>>>
>>>
>>--
>>====================================================
>>Ray Luo, Ph.D.
>>Department of Molecular Biology and Biochemistry
>>University of California, Irvine, CA 92697-3900
>>Office: (949)824-9528 Lab: (949)824-9562
>>Fax: (949)824-8551 e-mail: rluo_at_uci.edu
>>Home page: http://rayl0.bio.uci.edu/rayl/
>>====================================================
>>
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>
>
>--
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>.
>
>
> 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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