Are you sure the radii used in Molsurf and Sybyl/MSMS are the same?
linfu wrote:
>Dear Amber Community!
>
>my question is about SAS in MMPBSA.
>In MMPBSA, SAS is calculated by Molsurf.(1.4 A probe)
>surface area = 119.096 ## this is Solvent accessible surface area according to the mm_pbsa.in
>
>however i re-calulated the SAS using sybyl and MSMS.
>MSMS:
> Comp. probe_radius, reent, toric, contact SES SAS
> 0 1.400 4.649 46.343 72.564 123.556 266.854 ##
>SYBYL:
> Probe 1.4 A SES SAS
> 118.072 242.347 ##
>
>so i am confused about it. from the data above, it shows that the SAS in MMPBSA is SES (connolly surface)
>not the Solvent accessible surface area.
>
>Could anyone help me to figure out that what the SAS in the MMPBSA means exactly!
>
>THANK YOU IN ADVANCE!
>
>MM-PBSA(Molsurf)
>******************************************************
>MM
>GB
>PB
>MS
>1
> BOND = 0.6452 ANGLE = 3.4947 DIHED = 8.7404
> VDWAALS = -0.3062 EEL = 15.9468 EGB = -1.8703
> 1-4 VDW = 0.4943 1-4 EEL = -55.9851 RESTRAINT = 0.0000
>corrected reaction field energy: 0.0000 kt
> corrected reaction field energy: -8.609024 kt
>surface area = 119.096
>*******************************************************
>
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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.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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Received on Sun Jun 11 2006 - 06:07:21 PDT
