AMBER Archive (2007)

Subject: RE: AMBER: MM-PBSA doubt

From: Ray Luo (rluo_at_uci.edu)
Date: Mon Jan 29 2007 - 22:04:52 CST

Mathew,

 

How did you set MS in the file "mm_pbsa.in" for each of the tests that you
did?

 

Best,

Ray

==========================================

Ray Luo, Ph.D.

Dept Molecular Biology & Biochemistry

University of California, Irvine, CA 92697

USPS: PO Box 3900

Phone: (949) 824-9528

Email: rluo_at_uci.edu

Web: http://rayl0.bio.uci.edu/

==========================================

 

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
mathew k varghese
Sent: Monday, January 29, 2007 6:13 PM
To: amber mail list amber
Subject: AMBER: MM-PBSA doubt

 

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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