Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 !

From: <>
Date: Fri, 9 Jul 2010 08:43:47 -0400 (EDT)


> Thanks for helping me....I want to know if, I am having two such ligand in
> which the charges have countable if 1stligand+protein
> complex is having a charge of 2 Na+ ions and the 2ndligand+protein complex
> does not have any charge.
> then what can be the solution to such problems..? These charges are added
> just for the sake of neutrality.

in such a case, were you change the system from one total charge to
another, you could either neutralize the first or the second system. You
should not neutralize both, unless you explicitly want to disappear the
ions together with changing your ligand and thereby include their
solvation free energy in the total deltaG, which for a typical application
you would not do.

Kind Regards,


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Fri Jul 09 2010 - 06:00:14 PDT
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