AMBER Archive (1999)

Subject: Problems for Energy 1,4

From: Pascal Bonnet (pascal_at_qorws1.uab.es)
Date: Tue Dec 21 1999 - 18:45:22 CST

Hi,

I have a molecule with dummy atoms situated between carbons (on the middle of
the C-C bond). So, this dummy atoms are included in the main chain.
The problem is with the vdW interactions, the energy is very large. The reason
is quite simple:

C1-C2-C3-C4 The interaction between C1 and C4 is 1-4vdW (scaled by a 0.5
factor)
but in adding the dummy atoms we obtain:
C1-D1-C2-D2-C3-D3-C4
Now, the interaction between C1 and C4 IS NOT CONSIDERED a 1-4 vdW (there are 6
bonds between them), so it is not scaled and the energy is very large and we've
got longer distances.

Is there any way to play a trick on the program in a way to obtain the same vdW
energy with and without dummies?

Thanks in advance.. 

-- 
Pascal Bonnet                       Tel: 34935811266 
Unitat Quimica Organica             Fax: 34935811265  
Facultat de Ciences                 Email pascal_at_qorws1.uab.es
Universitat Autonoma de Barcelona
08193 Bellaterra (Barcelona)
Catalunya