AMBER Archive (2005)

Subject: Re: AMBER: Connecting two molecules

From: Hwankyu Lee (leehk_at_umich.edu)
Date: Mon May 23 2005 - 11:51:20 CDT

Although I put information of some bonds (OH-p2, o-OH), I didn't make
frcmod (force constant and length) of P-N bond. I think gaff covers P-N
bond. This problem could happens because of force constant of other
bonds ??

best,
Hwankyu.

On May 23, 2005, at 11:23 AM, David A. Case wrote:

> 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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