VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Tue Mar 09 2021 - 11:19:20 CST

W dniu 09.03.2021 o 15:28, Prof. Eddie pisze:
> 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.

Just keep in mind that while for dihedral angles (7th column) one can
use any value, for valence angles (5th column) the range is limited to
(0, 180).

Pawel

> Thank you!
> Eddie
>
> On Tue, Mar 9, 2021 at 5:51 AM Pawel Kedzierski
> <pawel.kedzierski_at_pwr.edu.pl <mailto: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