Dear amber，
I have a few questions about MM-PBSA in Amber 8, and hope somebody could help.
1. The value of "PROBE" parameter.
I see the statement like this in the example of manual:
---------------------------------------------------------------------
.MS
#
# Molsurf parameters (this section is only relevant if MS = 1 above)
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# Since Bondi radii are already augmented by 1.4A, PROBE should be 0.0
#
PROBE 0
#
---------------------------------------------------------------------
I'm not pretty sure the meaning of bondi radii, and where it is used, and whether it should be set 0 in any case.
2. The "SURFTEN" and "SURFOFF" parameters in PB section.
I have seen a few different settings of these two parameters in others' papers, such as 0.00542 and 0.092, 0.00542 and 0.92, 0.005 and 0, I wonder which setting is appropriate on earth while delphi is used.
3. "RADIOPT".
The example says that a value of 0 uses the cavity radii from the prmtop file, and a value of 1 sets up optimized cavity radii at the pbsa initialization phase. I wonder which one is better for the case of protein-protein interaction.
Thanks a lot!
Best regard!
zgleo
2005-12-02
___________________________________________
Zhiguo Liu
Ph.D candidate
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
Chinese Academy of Science
Shanghai, China
zhiguo.leo.gmail.com
zgliu.sibs.ac.cn
___________________________________________
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Received on Fri Dec 02 2005 - 05:53:01 PST
