AMBER Archive (2007)

Subject: Re: AMBER: bad atom type errors in GB for halides?

From: David A. Case (case_at_scripps.edu)
Date: Thu Apr 12 2007 - 19:04:55 CDT

On Thu, Apr 12, 2007, David Mobley wrote:
>
> This is probably naive, but I'm trying to run some simulations of
> various small molecules in GB solvent. This includes some things like
> bromomethane, etc. I can set them up fine with tleap (no
> warnings/errors), but when I go to run in GB solvent, I get an error
> like "bad atom type: br".

This message is coming from the surface area term, not from GB itself. Amber
uses the LCPO parameterization of surface area terms, and these are not
available for all atom types. If it fits your needs, you might try setting
gbsa=0.

....dac

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