AMBER Archive (2006)

Subject: Re: AMBER: Amber 9 installation problem

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Thu Oct 19 2006 - 14:13:58 CDT

Hi Prof. Case,
 
I guess I was tired enough to compare partial atomic charges side-by-side, rather than matching their atom names first.
 So the sustiva test is fine too.
 Thanks for clearing things out for me. I can now sleep well.
 
 regards,
 
 jenk.
 
  
"David A. Case" <case_at_scripps.edu> wrote: On Thu, Oct 19, 2006, Cenk Andac wrote:

> One thing however I do not understand is the antechamber test for sustiva.
> partial atomic charges show high deviations from reference values as seen
> below

> < 1 C1 0.728 1.403 0.255 ca 1 SUS 0.049
> ---
> > 1 C1 0.728 1.403 0.255 ca 1 SUS 0.050
> 10,11c10,11
> < 4 C3 0.290 0.932 0.158 c3 1 SUS 0.315
> < 5 C4 1.635 0.352 0.032 c1 1 SUS 0.196
> ---
> > 4 C3 0.290 0.932 0.158 c3 1 SUS 0.314
> > 5 C4 1.635 0.352 0.032 c1 1 SUS 0.197
> 21,22c21,22
> < 15 C9 0.117 1.500 1.582 c3 1 SUS 0.619
> < 16 F1 1.056 2.097 1.693 f 1 SUS 0.229
> ---
> > 15 C9 0.117 1.500 1.582 c3 1 SUS 0.620
> > 16 F1 1.056 2.097 1.693 f 1 SUS 0.228

I don't understand: the largest deviation between the "<" lines and the ">"
lines is 0.001(?)

....dac

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