VMD-L Mailing List

From: Wenhao Liu (mdsimulate_at_gmail.com)
Date: Wed Apr 17 2013 - 09:17:23 CDT

Chris,
So you mean I can set the weight like to 2 when I deal with oxygen-water
bonding in the condition that oxygen in my new molecule can form two
hydrogen bonds with water? Thank you!

Wenhao

在 2013年4月17日星期三，Mayne, Christopher G 写道：

> It is not required due to the symmetry of water--there is no extra
> information to be gained by flipping the identities of the hydrogens. ffTK
> handles the positioning of the water automatically.
>
> Regards,
> Christopher Mayne
>
>
> On Apr 17, 2013, at 1:53 AM, Wenhao Liu wrote:
>
> > Hello vmd people,
> > I was just wondering is it required to set up more than 1 hydrogen
> bonding for Acceptor (like the oxygen that can bonding with 2 hydrogen of
> the water) when I need to do the water interaction Gaussian calculation in
> charge optimization step? But I can only have 1 possible conformation to
> put water molecule bonding with oxygen in Acceptor indices, the other
> possible hydrogen boding between oxygen and hydrogen of water should be in
> different orientation, right? Or I can just set the weight of this
> calculation to 2 when I do the charge optimization? Thanks in advance.
> >
> > Wenhao
>
>