AMBER Archive (2008)

Subject: AMBER: addions and addions2

From: dpandit_at_brandeis.edu
Date: Tue Mar 25 2008 - 09:38:22 CDT

Hi All:
I am referring AMBER 9 manual and AMBER tutorials online. It is
mentioned in the Tutorial A8 - "Loop Dynamics of the HIV-1 Integrase
Core Domain" that it is better to use addions2 then addions so that
ions are not too near the protein. In the tutorial counter ions are
added after adding the solventbox. However, in the manual page number
48, there is only mention of addions and it is mentioned that it is
better to solvate after adding ions. I would appreciate if community
can share their opinion on this issue.

Thank you.
Deepa

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