From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Tue Sep 08 2015 - 15:10:03 CDT

The guessing algorithm gives you a decent place to start from; hopefully you would need to remove fewer entries than you would have had to add, and thus, saving you time.

The water molecules aren't actually bonded to your molecule. When loading in files that don't contain explicit bonding information, e.g., PDB, VMD employs heuristics to guess where the bonds are based on atom-to-atom distances; once the bonds are defined, they apply to all frames. Since the water is close to your molecule in the first frame of the optimization, VMD thinks there's a bond and applies is to all subsequent frames.

Regards,
Christopher Mayne

On Sep 8, 2015, at 2:57 PM, Chitrak Gupta wrote:

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<mailto: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=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.