AMBER Archive (2008)

Subject: AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params

From: Marcin Krol (krol01_at_cancer.org.uk)
Date: Tue May 13 2008 - 08:44:48 CDT

Dear All

I'm a bit confused what are the correct values for CAVITY_SURFTEN &
CAVITY_OFFSET parameters used in PB calculations. I want to calculate
free energy of binding with mm_pbsa.pl script. I wanted to use the
RADIOPT=1 and NPOPT=2.

AMBER manual says (on p. 271) that 'If NPOPT is set to 1 and RADIOPT set
to 1, these two lines (CAVITY_SURFTEN/CAVITY_OFFSET) can be removed,
i.e. use the default values set in pbsa for this nonpolar solvation
model. Otherwise, please set these to the following:
# CAVITY_SURFTEN: 0.04356
# CAVITY_OFFSET: -1.008'
I understand I should use 0.04356 and -1.008 if I use RADIOPT=1 and
NPOPT=2 and I don't need to worry if I use NPOPT=1

However, on p. 128 of the AMBER manual it is written that:
'CAVITY_SURFTEN ... The default value is for NPOPT = 2, but not for
NPOPT = 1.
CAVITY_OFFSET ... The default value is for NPOPT = 2, but not for NPOPT
= 1.'
So now it looks like I don't need to worry if I use NPOPT=2 but should
define CAVITY values if I use NPOPT=1

Could you comment on this? Is Sander clever enough to apply appropriate
CAVITY values both for NPOPT=1 and NPOPT=2 and I don't need to worry too
much? Or is the manual wrong in one place (which one?)

Cheers
Marcin 

-- 
Dr Marcin Krol
Biomolecular Modelling Laboratory
Cancer Research UK
London Research Institute
44 Lincoln's Inn Fields
London WC2A 3PX

Telephone: 020 7269 3033
Fax:       020 7269 3258
E-mail: marcin.krol_at_cancer.org.uk

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