AMBER Archive (2008)

Subject: AMBER: pdb file ??

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Thu Aug 21 2008 - 01:21:47 CDT

Hi
It is the water-molecule system.
For a molecule, like R-N(CH3)3-Br, I could make a pdb file either include Br ion or exclude Br ion.

If I exclude Br ion, I have to make Br ion as the counter ion for my system.
If I include Br ion, I do NOT have to make Br ion as the counter ion since it will automatically become the counter ion.
Am I right?

Thank you
Lin

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