AMBER Archive (2005)

Subject: Re: AMBER: GBSA calculation

From: David A. Case (case_at_scripps.edu)
Date: Mon Feb 28 2005 - 11:48:24 CST

On Mon, Feb 28, 2005, Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) wrote:
>
> I tried to perform GBSA calculations, and set igb=1, gbsa=1 in the
> input namelist.
> The result was that I obtained an error mesage saying Bad atom Type IM.

The GBSA implementation in Amber only knows about certain types of atoms.
The code would have to be modified to teach it about new atom types.

I'm not sure that it makes much sense to use a surface-area model for
ions(?!?). We generally have no experience even with using the GB model
itself with explicit ions. So, you should expect to have to modify the
code to get the sort of simulation you want, and you should expect to have to
check carefully that the results you get made good physical sense.

....dac

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