Re: AMBER: Poisson Boltzmann dynamics error

From: Rachel Burdge <>
Date: Thu, 10 Feb 2005 12:51:05 -0600

Yes, I did just realize that- I'm planning on using generalized born
instead, but thanks for your response!


On Tue, 2005-02-08 at 06:13, Ray Luo wrote:
> Rachel Burdge wrote:
> >I am trying to run MD of a 53,059 atom system with a restraint on part
> >of the protein. I solvated using a cap around the area of interest, and
> >tried to run MD using igb = 10, which calculates a reaction field for
> >the system, and the run crashes. Alternatively, this same system works
> >fine with Generalized Born (igb = 1).
> >
> Hi Rachel,
> I'm not sure I understand what you want to do. Are you trying to solvate
> only a small portion of your protein with cap water in PBMD? As
> described in the manual PBMD is only supported by developers when the
> protein if fully solvated in cap water.
> Best,
> Ray

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Received on Thu Feb 10 2005 - 19:53:00 PST
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