AMBER Archive (2005)

Subject: Re: AMBER: how to cap regions

From: David A. Case (case_at_scripps.edu)
Date: Thu Mar 31 2005 - 09:45:26 CST

On Wed, Mar 30, 2005, S.Sundar Raman wrote:

> i read the biotin streptavadin tutorial.
> i would like to know how you gave value for cap command.
> how to calucluate that regions position.
> when satrted to minimise it, it says ewald parameter are exceeded the
> limits.how can i solve this problem

In modern versions of Amber, the default value of ntb is 1, indicating a
periodic simulation. You need to set this to zero for a cap simulation.

I will update the tutorial file, which came from an earlier version of the
code.

...thanks for the report...dac

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