AMBER Archive (2007)

Subject: AMBER: MM-PBSA doubt

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Mon Jan 29 2007 - 20:12:44 CST

Dear AMBER users,

I have a question about the mm-pbsa calculation of free energy.
I have tried the calculation with different parameters for SURFTEN, SURFOFF and CAVITY_SURFTEN , CAVITY_SURFOFFSET. When I use the values

 for SURFTEN = CAVITY_SURFTEN=0.00542
and SUROFF=CAVITY_SURFOFFSET=0.92,

I got comparable values for PBTOT and GBTOT.
My RADIOPT=0 and NPOPT= 1,
So when I used the values of

CAVITY_SURFTEN 0.00542
CAVITY_OFFSET 0.92
#
SURFTEN 0.04356
SURFOFF -1.008
as specified in the manual, I got much difference between PBTOT= -38.00(3.05) and GBTOT=-15.58 (1.97)

SURFTEN= 0.0072 and SUROFF = 00 is used in the GB section.

Which values should I use for the use of GB and PB calculations?
My system is a small molecule bind to a DNA with 12 basepairs

Please help me.

Thanking you,

Mathew K Varghese

                                 
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