AMBER Archive (2007)

Subject: AMBER: Some questions on mm_pbsa

From: Hu, Shaowen (JSC-SK)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Fri May 18 2007 - 09:53:35 CDT

Dear All,

I have some questions on the mm_pbsa calculation with AMBER9:

1. Are the STDs of the output file "*_statistic.out" the standard
deviation of the distribution or the standard deviation in the mean?

2. What is the "corrected reaction field energy" in the output file
"*_com.all.out"? How does it relate to PBCAL?

3. To do the separate trajectories calculation, the interactions between
the receptor A and ligand B is obtained by <AB>-(<A>+<B>) or <AB-(A+B)>?

Thank you very much for your assistance.

Shaowen Hu, Ph.D.
Research Scientist
USRA Division of Space Life Sciences
3600 Bay Area Blvd., Houston, TX 77058, USA
Phone: 281-483-1163
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