VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Tue Mar 09 2021 - 08:28:34 CST

Hi all,
Thank you! Moving the atoms in vmd did not work as it did not write the
changed atoms. But changing the angles does work easily. Adding 180 to the
angle for the water's first line angle (second entry) was very effective.
Thank you!
Eddie

On Tue, Mar 9, 2021 at 5:51 AM Pawel Kedzierski <pawel.kedzierski_at_pwr.edu.pl>
wrote:

> 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
> <https://urldefense.com/v3/__https://en.wikipedia.org/wiki/Z-matrix_(chemistry)__;!!DZ3fjg!qzw6lIYUbCqZ59nzaRVi9UX4uUxf96vpvoNor9rBthuD7i2ucl02OYx0cM6pD-NpiA$ > 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.
>
> Cheers,
>
> Pawel
>
> Thanks for the help!!
> Eddie
>
> --
> _________________________________________________________
> Edward Ackad, Ph.D
> <https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!srQPZ1jc311MKadXRrCkW9cOwjF2nJe5oOtA73jdIscAX1onhY341wS-s5OBmicW7Q$>
> Associate Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390
>
>
> 

-- 
_________________________________________________________
Edward Ackad, Ph.D <https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!qzw6lIYUbCqZ59nzaRVi9UX4uUxf96vpvoNor9rBthuD7i2ucl02OYx0cM5M-Yx9pA$ >
Associate Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390