Bugs item #1043797, was opened at 2004-10-10 03:24 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1043797&group_id=23629
Category: File Input/Output Group: None Status: Open Resolution: None Priority: 5 Submitted By: Miguel (migueljmol) Assigned to: Miguel (migueljmol) 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] > ----- > ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1043797&group_id=23629 ------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
