AMBER Archive (2005)

Subject: Re: AMBER: rborn(i) in egb.f

From: David A. Case (case_at_scripps.edu)
Date: Tue May 03 2005 - 17:59:23 CDT

On Tue, May 03, 2005, Harianto Tjong wrote:

> I have tried it, but I have no clue whether this set of radii for EGB
> calculation (igb=2)
> are the same as those from ambpdb -r.
> I could not see what igb=2 uses as input radii parameter, but definitely
> I could see ambpdb -r result.

Look at the "radii" section in the prmtop file.

>
> Furthermore in egb.f, I read:
> "(rborn(i) - offset)*si "
> Can you give me the reference to find out the mutual overlaps scaling
> factor 'si' ?

Look at the "screen" section in the prmtop file. See also Table 1 in
Ref. [43] in the Amber manual.

...dac

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