From: Pawel Kedzierski (
Date: Tue Mar 09 2021 - 05:51:15 CST

Dear Edward,
W dniu 08.03.2021 o 15:46, Prof. Eddie pisze:
> Hi all,
> I've gone through the fftk tutorials and they tell you to check the
> placement of the waters before running the gaussian files. Good
> advice. I found that a few of my waters would overlap with some of the
> ligand atoms. However, now I am not sure what to do? Do I just not
> optimize those atoms or is there a way to "fix" this? I'm
> unfamiliar with gaussian and don't have gaussview.

If you look inside such FFTK-prepared Gaussian input file you will see,
that after the cartesian coordinates of your parametrized molecule the
water is placed using internal coordinates in Z-Matrix format
<;!!DZ3fjg!tsJXp_IbYX27BfQ9U7JV-4KQhC6zDwd69lLsve8BOWMudGdDKcHmMWK2gQqOek1ozQ$ > in such I way, that
the only variables to optimize are the atom-water distance and a
dihedral describing the rotation of the water around the atom-water
axis. It is relatively easy to "fix" the position of water manualy, for
example by changing the angle at which this water approaches the subject
atom, flipping it to the other side of a ring etc. The same button "Load
Gaussian input files" which you used to inspect the generated geometry
is useful to check you changes visually. In cases there are several
waters against the same atom (like for carbonyl oxygens) you can get rid
of some of them. The idea is to have the water closer to the single
relevant atoms than to other ones so the interaction energy will not
contain significant contribution from the neighbours. The strength of
FFTK is that you will be able to quantify the error later on using COLP
so if it's not acceptable, you can get back and try to do it better.



> Thanks for the help!!
> Eddie
> --
> _________________________________________________________
> Edward Ackad, Ph.D
> <*7Eeackad__;JQ!!DZ3fjg!srQPZ1jc311MKadXRrCkW9cOwjF2nJe5oOtA73jdIscAX1onhY341wS-s5OBmicW7Q$>
> Associate Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390