VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Sun May 24 2020 - 21:24:40 CDT

Thanks,

I managed to flip it by editing the dihedral in the text file, and verified
by visualising in FFTK-VMD. None of my molecular editors (Chem3D, Avogadro,
SPARTAN, Discovery Studio, Molefacture) could read the file unless I
renamed the dummy atom to a real element. If I replaced it with D, Chem3D
would read it but it didn't interpret the Z-matrix properly leading to some
weird coordinates. Can you suggest an editor that can read it properly?

Also, in the case that no position is free of secondary interactions (e.g.
quaternary carbon in 3-substituted indole) do I simply not probe that atom?
What threshold should I use for determining whether it's acceptable to
probe or not?

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Sat, 23 May 2020 at 04:53, Aleksei <erdelgado_at_udec.cl> wrote:

> Is not against protocol, you are supposed to minimize the secondary
> interactions.
>
> You can edit the input file using any molecular editor, the water
> molecule's coordinates are defined using a Z-matrix, so it suffices to
> modify the dihedral of the first atom (either an hydrogen or a dummy
> atom) to move the whole water molecule.
>
>
>
> El 22/5/20 a las 2:24, Daniel Fellner escribió:
> > While running the Gaussian input files, one of the calculations ran into
> a
> > segmentation violation error. Upon visually inspecting the initial
> > coordinates of the water, it appears that it's very close to one of the
> > other rings in my system. Is there some way to manually place this on the
> > other side (the opposite site of the ring is unobstructed)? Or would that
> > not be according to protocol? If not, how should I proceed?
> >
> >
> > *Daniel Fellner BSc(Hons)*
> > PhD Candidate
> > School of Chemical Sciences
> > University of Auckland
> > Ph +64211605326
> >
>
>