AMBER: Questions about MM-PBSA in Amber8

From: zgleo <>
Date: Fri, 2 Dec 2005 13:04:26 +0800

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:
# 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
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.

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!

Zhiguo Liu
Ph.D candidate
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
Chinese Academy of Science
Shanghai, China

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Received on Fri Dec 02 2005 - 05:53:01 PST
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