AMBER Archive (2006)

Subject: Re: AMBER: anal vs sander

From: David A. Case (case_at_scripps.edu)
Date: Fri Jan 27 2006 - 17:28:51 CST

On Fri, Jan 27, 2006, Piotr Cieplak wrote:

> No, I used eps 1.0. The input for anal is as follows:
>
> test of anal energies
> 1 0 0 0 0 1
> 0 0.0 0.0 0.0 0.0
> 1 0 0 0 0 0
                              ^^^^^

You are setting idiel=0 in anal, which means a distance-dependent dielectric.
But GB uses a constant dielectric. Try setting this value to 1.

[Of course, this awful user interface is one reason anal should be headed for
the junkpile. But the promised replacements have been slow in arriving....]

....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu