AMBER Archive (2007)

Subject: RE: AMBER: MM-PBSA doubt

From: Ray Luo (rluo_at_uci.edu)
Date: Mon Jan 29 2007 - 23:29:01 CST

Mathew,

 

If you set MS to 1, only SURFTEN and SURFOFF are used for MS calculations
for PB, CAVITY_SURFTEN and CAVITY_SURFOFFSET are used for PB only when MS is
set to 0. Please see the mm_pbsa input file for more explanation.

 

So if you use different SURFTEN and SURFOFF between PB and GB, you will get
different nonpolar solvation energies. If you use the same SURFTEN and
SURFOFF, you will get the same solvation energies. If you want to compare
PBSA and GBSA, you'd better stay with the same MS parameters.

 

All the 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 8:23 PM
To: amber_at_scripps.edu
Subject: RE: AMBER: MM-PBSA doubt

 

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_at_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_at_uci.edu

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

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

 

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-ambeer_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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/\/\athew

Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India

email mathew_kvarghese_at_yahoo.co.in

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

  

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