VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Tue Sep 08 2015 - 14:57:55 CDT

Hi Christopher,

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.

Regards,
Chitrak.

On Tue, Sep 8, 2015 at 1:48 PM, Mayne, Christopher G <cmayne2_at_illinois.edu>
wrote:

> Chitrak,
>
> This topic has been discussed very recently:
>
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/26080.html
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_mailing-5Flist_vmd-2Dl_26080.html&d=AwMFAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=wF2NhQZUqE_YMsbjgIM_pn5EzgUuDU4489TyIrVxZMA&m=nxdnwoVkBAlKo6C5YLtAkURGX7u5dduUPtsDXBZtARg&s=pB6bMmybO11TVe1NjdXJtzcxEWwX7jpLnGeR6UteoQk&e=>
>
>
> Regards,
> 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?
>
>
> Regards,
> Chitrak.
>
>
>