AMBER Archive (2006)

Subject: Re: AMBER: GBSA EGB = NaN

From: David A. Case (
Date: Mon Aug 21 2006 - 13:21:10 CDT

On Mon, Aug 21, 2006, William Wei wrote:

> > Try igb=1 just on a single snapshot, to see if the NaN problem goes away.

> Thank you very much, Dr. Case. It solve my problem. I read the amber
> manual, but still did not get wich option I should use for my issue. Do you
> have any general idea that which version of GB is good for which kind of
> system.

The igb=3,4 options in amber7 were removed in later versions. They were
implementations of models created by Jayaram and Beveridge, and probably were
not widely debugged. At this point, tracking down what is wrong with the code
may not be something at anyone wants to do. If you cannot upgrade, setting
igb=1 is probably the safest course for amber7.

You can read about more recent options in the Amber 9 Users' Manual, available
on-line at the Amber web site.


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