AMBER Archive (2005)

Subject: AMBER: pbsa problem

From: Suxin Zheng (sxzheng_at_u.washington.edu)
Date: Wed Jul 27 2005 - 14:47:29 CDT

Dear amber and Luo,
First,
I have read your reply about the pb bomb when radiopt=1. I still not
clear how to set the radii prmtop for small molecules using a perl
script.
Second,
Now I use radiopt=0 for pbsa calculations. But my system has higher
negative charges. When calculating the MM energy with cut = 999.0,
the MM electronic energy will be positive. Even adding the PB item,
the PBTOT will be positive. How to deal this problem.

Thank you
suxin
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