AMBER: scaling 1-4 NB interaction for rings

From: <>
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 ?

       / \
      / \
     a5 a2
     | |
     | |
     b4-- b3

There are two paths connecting these atoms.

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?

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