AMBER Archive (2006)

Subject: Re: AMBER: Na+ with GB/SA?

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 12 2006 - 16:24:17 CST

On Thu, Jan 12, 2006, Steve Gwaltney wrote:
>
> I am trying to model some protein-ligand interactions. It is believed
> that a sodium ion resides in the active site of the protein, and
> therefore I am trying to include it in the calculations. However, if I
> set "GBSA=1," the calculation crashes with the message
> "bad atom type: IP." A plain GB calculation works fine. Is there a
> workaround to this problem?

You would need to modify src/sander/mdread.f to provide LCPO parameters
for Na+. Ideally, you would fit these to correctly computed surface areas for
a number of "typical" sodium-ion-water-protein geometries. In practice,
you might be able to estimate these by analogy or some other simpler way.

...good luck...dac

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