Dear Luo,
Thanks for the reply.
I have set MS=1 and PB and GB= 1 for the calculations.
I have doubts about the values of CAVITY_SURFTEN and CAVITY_SURFOFFSET to be used. Again , Should I use the same SURFTEN and SURFOFF for PB as well as GB?
Thanking you,
Mathew.
Ray Luo <rluo.uci.edu> wrote: 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.uci.edu
Web: http://rayl0.bio.uci.edu/
==========================================
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.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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/\/\athew
Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India
email mathew_kvarghese.yahoo.co.in
===========================================================================
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Received on Wed Jan 31 2007 - 06:07:31 PST
