AMBER Archive (2002)

Subject: How to choose the box and cap size

From: sxzheng (sxzheng_at_mail.shcnc.ac.cn)
Date: Thu Oct 31 2002 - 00:42:27 CST

Dear all,
 I find there is some different size used in FEP calculation,such as 10 or 12 A of the boxsize and 20 or 25A of the cap size.I want to use solvatecap the complex and the solvatebox the ligand to calculate the dG,then what is the size I should choose in the calculations.
Thank you
sxzheng