Dear Amber users:
Question regarding scaling 1-4 non-bonded interactions for rings:
I would like to know how the vdw and electrostatic interactions
are to be scaled for atom pairs, such as a1-a3 and b1-b4
in 5 and 4-membered rings as depicted in the Figure ?
a1
/ \
/ \
a5 a2
| |
a4---a3
b1---b2
| |
b4-- b3
There are two paths connecting these atoms.
5-mem:
If a1-a2-a3 is selected, vdw a1-a3 is suppressed.
On the contrary, if a1-a5-a4-a3 is selected, vdw a1-a3 is scaled by 1/SCNB.
Which rule should be applied?
4-mem:
What about vdw b1-b4?
Alternatively,is there any specific rule used for such small sized rings?
Surely the prescription should depends on how FF parameters have been tuned.
Thanks in advance for your help.
---------------------------------
Dr Jiro Shimada, FRL, NEC Corp.
34, Miyukigaoka, Tsukuba, 305-8501, Japan
(E-Mail:j-shimada.az.jp.nec.com)
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Sep 29 2004 - 15:53:00 PDT
