Re: Re: AMBER: delphi and surface in MMPBSA

From: Yong Xu <yxu.mail.sioc.ac.cn>
Date: Fri, 21 Oct 2005 9:9:7 +0800

Dear Prof. Case

======= 2005-10-20 09:06:00 David A. Case wrote=======
there are always different output for those two program using the same
probe-radius. for molecule no100.pdb, MMPBSA give out 78.269 with 1.4 A probe-radius
>>
>> BUT MSMS give out following infomation, which surface should be taken ?
>> ========
>> command : msms -if no100.xyzr -probe_radius
>>
>> ANALYTICAL SURFACE AREA :
>> Comp. probe_radius, reent, toric, contact SES SAS
>> 0 1.500 1.976 24.483 57.351 83.810 213.956
when I use probe_radius 1.40, the result is
ANALYTICAL SURFACE AREA :
    Comp. probe_radius, reent, toric, contact SES SAS
      0 1.400 1.834 23.714 58.271 83.818 203.611
..........
NUMERICAL VOLUMES AND AREA
    Comp. probe_radius SES_volume SES_area)
       0 1.40 56.304 77.388
    Total ses_volume: 56.304
MSMS terminated normally

which number should be taken for SA*0.00542+0.92 calculation, 77.388 or 83.818 ???
I think the former is closer to value 78.269 given by Molsurf in MMPBSA/AMBER.
>
>Note that you have a 1.4 Ang. probe for molsurf and a 1.5 Ang. probe for MSMS.
>
>The "molecular surface area" is called SES (solvent-excluded surface) in MSMS.
>If you actually use the same probe radii, you should get comparable results
>from the two programs.
>
>You can get the solvent-accessible surface (SAS) area from molsurf by the
>following: add the probe radius to each of the atomic radii, then compute the
>resulting molecular surface area with a probe radius of zero.
what kind of surface are used for SA*0.00542 + 0.92 calculation by Molsurf in MMPBSA/AMBER?


>
>....good luck...dac
>
>--
>
>==================================================================
>David A. Case | e-mail: case.scripps.edu
>Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>The Scripps Research Institute | phone: +1-858-784-9768
>10550 N. Torrey Pines Rd. | home page:
>La Jolla CA 92037 USA | http://www.scripps.edu/case
>==================================================================
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= = = = = = = = = = = = = = = = = = = =
                        

Best regards!
                                 
        Yong Xu
        yxu.mail.sioc.ac.cn
          2005-10-21
===========================================================
* Yong Xu
* State Key Lab of Bioorganic & Natural Product Chemistry
* Shanghai Institute of Organic Chemistry
* Chinese Academy of Science
           
* 354 Feng Lin Road, Xu Hui District
* Shanghai, 200032, China
        
* Email: yxu.mail.sioc.ac.cn
* yxuemail.sina.com
===========================================================
      


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Received on Fri Oct 21 2005 - 02:53:02 PDT
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