AMBER Archive (2005)

Subject: AMBER: MM_PBSA_parameter

From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Wed Nov 23 2005 - 13:48:12 CST

Hi all,

I am using MM_PBSA to calculate the binding free energy of a glycoprotein
system. The atom number is about 10,000.

First of all, I tested MM_PBSA using the files in the "Example" fold. PB is run
by pbsa within Amber8. I got the same result as that in the fold with GB and
almost the same result with PB. Then I ran MM_PBSA for my system. Due to the
large size of my system, I have to decrease the "SCALE" to 1.5. The topology
file I use is generate by tleap with default parameters. Total 150 snapshots
extracted from 3ns trajectory. The GB gives a negative value with small SD. But
PB gives a large positive value with large SD. I do not know what is wrong.
Then I tried to change some parameters. I set "PRBRAD" to 1.5 or 1.4. I got
very different answers. So my question is how to choose "PRBRAD". What does it
exactly mean to "use 1.4 with the PARSE parameter set and 1.6 with the radii
optimized by R. Luo"? What is PARSE parameter set and what is R. Luo parameter
set?

Another question is how I can make sure the solution of PB already converges if
I only set "LINIT" to certain number. Why is the "SURFTEN" different for PB and
GB? Why do we calculte the absolute reaction field energy ("REFE"=0) instead of
the difference of reaction field energy ("REFE">0) to calculate the binding
free energy?

Thank you in advance!

Wei Chen
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