VMD-L Mailing List

From: Aleksei (erdelgado_at_udec.cl)
Date: Thu May 28 2020 - 01:39:15 CDT

El 24/5/20 a las 22:24, Daniel Fellner escribió:
> 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?
My bad, seems only GaussView can handle the input files.
> 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?
For atoms that can't be probed the parameters are assigned by analogy.
If the parameters don't already exist you use a divide and conquer
approach and break your molecule into model compounds having your groups
of interest or similar structures. This also makes the parametrization
of force constants and dihedrals more tractable.
> What threshold should I use for determining whether it's acceptable to
> probe or not?
There is not a set treshold, but in case it isn't visually obvious look
for outliers in the interaction energy or distance.
>
>
> *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
>>>
>>