AMBER Archive (2006)

Subject: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ????

From: linfu (linfu3200_at_mail.sioc.ac.cn)
Date: Fri Jun 09 2006 - 22:25:24 CDT

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
*******************************************************

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