AMBER: scaling 1-4 NB interaction for rings

From: <j-shimada.az.jp.nec.com>
Date: Wed, 29 Sep 2004 23:16:38 +0900

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)
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Received on Wed Sep 29 2004 - 15:53:00 PDT
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