AMBER Archive (2006)

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

From: linfu (linfu3200_at_mail.sioc.ac.cn)
Date: Sat Jun 10 2006 - 22:27:20 CDT

Professor David A. Case and Ray Luo,Thank you very much for your answering.
i am using MMPBSA in amber7. not amber8 or amber9
here is the MS part of parameter setup in MMPBSA script.

@MS
#
# Molsurf parameters (this section is only relevant if MS = 1 above)
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# RADII - Name of the radii file.
#
PROBE 1.4
RADII ./atmtypenumbers
#
*****************************************************************
for MSMS
i using 1.4 A probe with density of 3.0 vertexes/ A^2

for SYBYL

i using 1.4 A probe with density of 3.0 vertexes.(connolly surface)
        

======= 2006-06-11 02:24:29 =======

>On Sat, Jun 10, 2006, linfu wrote:
>
>>
>> In MMPBSA, SAS is calculated by Molsurf.(1.4 A probe)
>
>I don't think this is correct. According to the manual, the probe radius
>should be set to zero, which is required to get an SAS from the molsurf
>program. See the comments and instructions in the "MS" section of the
>mm-pbsa chapter in the users manual (p. 292 for Amber 9).
>
>As Ray Luo suggested, you will have to be more specific about what radii and
>parameters you used, both for mm-pbsa and for the sybyl/MSMS calculation.
>Note also that you can run molsurf "by hand" (outside the mm-pbsa script)
>to experiment about what results it is giving.
>
>...good luck...dac
>
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