[AMBER] Adding Ions.

From: Ajay Ummat <ajayummat.gmail.com>
Date: Wed, 30 Jun 2010 14:05:25 -0400

I want to add 150mM Na+ Cl- ions in my system. I used the command: addions x
Na+ 91 Cl- 96 (as my system had +ve 5 charge and I needed 96 each of Na+ and
Cl-). When I visualize the result of adding ions, leap has added all the
ions only on one particular side of the protein. This certainly seems
unreasonable. Can anyone suggest me a way of uniformly distributing the ions
around the protein. When I say uniformly I mean to consider eletrostatics of
the distribution. A skewed distribution of charges would make my production
run unrealistic and unreliable. Thanks in advance.
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Received on Wed Jun 30 2010 - 11:30:03 PDT
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