AMBER Archive (2006)

Subject: Re: AMBER: anal vs sander

From: David A. Case (case_at_scripps.edu)
Date: Fri Jan 27 2006 - 15:33:57 CST

On Fri, Jan 27, 2006, Piotr Cieplak wrote:
>
> I minimized a protein using infinite cutoff , and igb=2 (gb/sa +
> saltcon=0.2) and then the last structure I reanalized using ANAL program..
> For this given particular structure I got all energy components the same
> besides 1-4 elstat and elstat , which in the case of GB/SA were 4 times
> larger values.
>
> I used in both cases the same cutoff. And I know that anal is decomissioned...

Is it possible that you set a dielectric of 4 in the ANAL input?
(This would be the last number on line 5 of the anal input)

...dac

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