Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system

From: David A. Case <>
Date: Fri, 18 Aug 2006 11:35:04 -0700

On Fri, Aug 18, 2006, Suxin Zheng wrote:

> If we want to consider the salt concentration, what's the range of
> the salt concentration in PB and GB calculation should be reasonable
> or acceptable.

This usually depends on what experiments you are trying to interpret.
"Physiological" salt concentration is generally something like 150 mM.

> Can we short the "cutoff" in MM calculation and PB or GB calculation,
> such as from 999 to 25. (thus the GB or PB total may be negative)
> Dose it make sense.

This is not a good idea, in my view. Electrostatic cutoffs can introduce
large and arbitrary changes to the energetics.


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Received on Sun Aug 20 2006 - 06:07:20 PDT
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