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

From: case <>
Date: Fri, 9 Jul 2010 08:36:01 -0400

On Fri, Jul 09, 2010, sunita gupta wrote:
> 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.

The "sake of neutrality" is probably not what you need to worry about most.
If I understand your situation, the two enpoints differ in charge by 2 units;
this is a big change, and you might want to consider whether you would be able
to really interpret the final result (e.g. could compare to experiment). But
there is no reason to require that the charges of the two enpoints be equal:
we use softcore TI all the time to change charge states (although usually only
by one unit of charge).

If you really want, you could try to simultaneously change the protein/ligand
complex *and* the two sodium ions (i.e. put the ions into the softcore
region). But the convergence problems then would be horrendous, and it's hard
to see (not knowing many details) how this would be better than not adding
the "extra" counterions.


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Received on Fri Jul 09 2010 - 06:00:11 PDT
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