AMBER Archive (2005)

Subject: Re: AMBER: mm_pbsa

From: Ray Luo (rluo_at_uci.edu)
Date: Sat Nov 12 2005 - 02:09:13 CST

Okay, could you email me your output and log files for your mmpbsa script?

Best,
Ray

Wei Chen wrote:

>Hi Ray,
>
>I didn't use Delphi. I used pb program in Amber8. I find a problem. I check the
>
>values of "corrected reaction filed energy". Its mean is not equal to
>the "PBCAL". Why is that?
>
>Thank you!
>
>Wei
>
>ÒýÓÃ Ray Luo <rluo_at_uci.edu>:
>
>
>
>>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
>>>>>
>>>>>--
>>>>>
>>>>>-----------------------------------------------------------------------
>>>>>The AMBER Mail Reflector
>>>>>To post, send mail to amber_at_scripps.edu
>>>>>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>>>>
>>>>>.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>--
>>>>====================================================
>>>>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/
>>>>====================================================
>>>>
>>>>-----------------------------------------------------------------------
>>>>The AMBER Mail Reflector
>>>>To post, send mail to amber_at_scripps.edu
>>>>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>>>
>>>>
>>>>
>>>>
>>>>
>>>--
>>>
>>>-----------------------------------------------------------------------
>>>The AMBER Mail Reflector
>>>To post, send mail to amber_at_scripps.edu
>>>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>>
>>>.
>>>
>>>
>>>
>>>
>>>
>>--
>>====================================================
>>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/
>>====================================================
>>
>>-----------------------------------------------------------------------
>>The AMBER Mail Reflector
>>To post, send mail to amber_at_scripps.edu
>>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>
>>
>>
>
>
>
> 

-- 
====================================================
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/
====================================================

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu