From: mathew k varghese <>
Date: Tue, 30 Jan 2007 04:22:50 +0000 (GMT)

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,


Ray Luo <> wrote: Mathew,
  How did you set MS in the file “” for each of the tests that you did?
  Ray Luo, Ph.D.
  Dept Molecular Biology & Biochemistry
  University of California, Irvine, CA 92697
  USPS: PO Box 3900
  Phone: (949) 824-9528
  -----Original Message-----
 From: [] 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
 I got comparable values for PBTOT and GBTOT.
 My RADIOPT=0 and NPOPT= 1,
 So when I used the values of
 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
  Here’s a new way to find what you're looking for - Yahoo! Answers


Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
Kottayam, Kerala


 Here’s a new way to find what you're looking for - Yahoo! Answers
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Received on Wed Jan 31 2007 - 06:07:31 PST
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