VMD-L Mailing List
From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Tue Sep 08 2015 - 14:57:55 CDT
Thanks for directing me to this link.
So from what I understand, for anything but really small molecules, it is a
good idea to use your chemical intuition to select donor and acceptor
atoms, is that correct?
I re-did this step, this time manually selecting the donors and acceptors.
However, I still have a few waters moving away from the molecule but are
still bonded to it, resulting in unrealistic bond lengths.
On Tue, Sep 8, 2015 at 1:48 PM, Mayne, Christopher G <cmayne2_at_illinois.edu>
> This topic has been discussed very recently:
> Christopher Mayne
> On Sep 8, 2015, at 10:54 AM, Chitrak Gupta wrote:
> Hi! I am new to the FFTK plugin. I am following the steps of the tutorial
> but having problems at the water interaction stage. I used the "Auto detect
> indices" to select the hydrogen bonding atoms. It included even Hydrogens
> bonded to aliphatic C, and atoms like amide C, carboxyl C, etc. There were
> also atoms that were included both in lists of donors and acceptors. Is
> that normal?
> After I ran the Gaussian calculations, some of the waters move away from
> the molecule. Some other waters also move away but are still bonded,
> resulting in severely elongate bonds. Does anyone know how to fix these?