Re: AMBER: Connecting two molecules

From: David A. Case <>
Date: Mon, 23 May 2005 08:23:51 -0700

On Mon, May 23, 2005, Hwankyu Lee wrote:
> 3) Connect N and P, and then when I did energy minimization with
> restraints of molecules, everything was fine. But, when I did
> energy-minimization without restraints of molecules, the connection
> between N and P was broken and went back to original configurations.
> H O
> | ||
> ---CH2-N P-O5'-DNA
> |
> OH

What are the force constant and equilibrium bond length for the P--N bond
that you are using? This should determine what sort of connection you get.

Note that force fields have no notion of whether or not this is really a
stable molecule or not, nor do Amber force fields make any use of bond orders.

....good luck...dac

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Received on Mon May 23 2005 - 16:53:00 PDT
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