Bugs item #1043797, was opened at 2004-10-09 20:24
Message generated for change (Comment added) made by hansonr
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Category: File Input/Output
Group: None
>Status: Closed
>Resolution: Later
Priority: 5
Submitted By: Miguel (migueljmol)
>Assigned to: Bob Hanson (hansonr)
Summary: z-matrix and dummy atoms
Initial Comment:
---------------------------- Mensaje Original
---------------------------- Asunto: Re: dummy atoms +
z-matrix
De: Ren� Kanters <[EMAIL PROTECTED]>
Fecha: Sat, 9 de Octubre de 2004, 8:42
Para: "Miguel" <[EMAIL PROTECTED]>
--------------------------------------------------------------------------
Hi Miguel,
In most programs I have seen X used for a dummy atom.
There are some other things that Gaussian input can
have: an atom what -Bq appended to it. The latter is
for ghost atoms, in which case one can set the
calculation to use the atom as the regular one, or as a
'ghost' where it only provides orbitals at that
location [no electrons or nucleus itself] to deteremin
what is called the Basis Set Superposition Error
(BSSE) with the Counterpoise method. I have never used
it, so I don't know how that is reported in the output...
About z-matrices, Gaussian has something about their
input on their web site:
http://www.gaussian.com/g_ur/m_molspec.htm
I also enclosed the description of the z-matrix input
from NWChem. That is more picturial, and with a bit of
geometry you should be able to calculate the
cartesians from that.
Since I mainly work with quantum mechanical
calculations and not
molecular mechanics, I never really have lone pairs as
input or output, but I recall that I have seen a
program in the distant past that used Lp for lone pairs.
Since I am taking a Java class, I was wondering whether
I could try to give it a go to write a java plug-in
for JMol. Can you point me more directly to a location
where I can find info about how to write a plug-in,
i.e., what class should it extend and what methods are
there for it, and how do I find information about
other things already in the structure(s), etc.?
Cheers,
Ren�
On Oct 9, 2004, at 6:40 AM, Miguel wrote:
> Rene wrote:
>
>> A dummy atom is an atom that is does not have a
nucleus or electrons, in other words it really is just
a place holder in space that can be used as a reference
point to define bonds, angles, and torsions in a z-matrix.
>
> This sounds familiar ... at least one person has told
me this before ...
> but I manage to forget
>
>> In a geometry optimization using a z-matrix the
z-matrix orientation is
>> in the output which has the dummies in them: they
have an atomic number
>> of -1. The standard orientation, I believe, is the
one you parse for and that one only real atoms, not
dummies. Enclosed is an output file that shows some of
this (x.log).
>
> I see that in your Gaussian 03 output and in k2.xyz
that the dummy atom is
> identified as element 'X' ...
>
> Q: Is 'X' *always* used as the element symbol for
dummy atoms for *all* programs?
>
>> About the representation, I believe that JMol
already has that set up. The problem I had is that they
are not recognized in a G03 z-matrix optimization file.
Enclosed is the concatenation of the xyz files that
NWChem gives for one of my calculations. The dummy atom
is the pink one
>> between the two carbons.
>
> Any element symbol that Jmol does not recognize
currently gets mapped to
> element 0 whose name is 'Xx' ... It is large, pink,
and has large covalent
> bonding radius so that it is easy to see. I intended
it to be used mostly
> for debugging.
>
>> This actually is also could work as an example
>> about my question of the graph. What I was wondering
there is the possibility to have, for instance, a
measurement like a CH bond distance be graphed against
a CCH angle in the molecule (to look for correlation in
their motion). This, of course, only works for a
multistep file.
>
> It sounds like this would be a good thing for someone
to add to the Jmol
> application, either embedded or as a plug-in.
>
>> Does this provide you with what you need wanted to know?
>
> There are two related items that probably should be
addressed at the same
> time.
>
> 1. Lone pair support ... another 'strange'
non-element point.
>
> 2. Z-matrix support ... everyone says that it is
easy, but I haven't done
> it yet.
>
>
> None of these things is going to happen until after
the official v10 release.
>
>
> Miguel
>
>
>
> -----
> Open Source Molecular Visualization
> www.jmol.org
> [EMAIL PROTECTED]
> -----
>
----------------------------------------------------------------------
>Comment By: Bob Hanson (hansonr)
Date: 2006-08-22 17:59
Message:
Logged In: YES
user_id=1082841
will reconsider if resubmitted
----------------------------------------------------------------------
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