From: Toshifumi Yui <tyui.cc.miyazaki-u.ac.jp>
Date: Tue, 20 Dec 2011 22:41:00 +0900

As working with tutorial 3 of MM_PBSA, I found the following message in the

igb=2 should be used with mbondi2 pbradii set.....

So I have carried out another trial calculations using a set of trmtop files
created with "set default PBradii mbondi2" command, which gave different
energy values for both GB and PB methods.
Also I've got the same message again in the FINAL_RESULTS_MMPBSA.dat file
produced by the trial calculations.

I wonder that I don't have to worry about this warning any way, and is this
Ok to use the trmtop files based on the normal PBradii setting according to
the tutorial, even using igb = 2 option ?
I am very confusing.

Thank you


Toshi Yui

AMBER mailing list
Received on Tue Dec 20 2011 - 06:00:04 PST
Custom Search