From: Conor B. <cbr...@ma...> - 2020-10-28 00:40:37
|
Hi John, Ah, I should have specified -- I had included some screenshots but removed them as the listserv seemed to not want such a large filesize. I'm running all of my calculations through the WebMO interface using Gaussian and the B3LYP/6-31G(d) basis. The molecule I'm currently looking at has the following chemical formula: C68H54N2O4P4(2+) (a singlet diradical naphthalene diimide with two diphenylphosphinoethane groups attached on the aromatic core). I've been getting the files directly from WebMO through its interface (i.e. going to the "all files" section on a specific job, selecting "binary", and then downloading the file). I'm wondering if there's something jmol doesn't like about the WebMO formatting of those output downloads, but that is entirely speculation. Hopefully that is the information you were looking for! Best, - Conor On Tue, Oct 27, 2020 at 6:13 PM John Keller <jwk...@al...> wrote: > Hi Connor, > > I’s be glad to offer advice, but it would help to know what kind of > molecule you’re working with, and which programs you’re using, besides > Jmol, to calculate and display NBOs? > > John Keller > > Dept of Chemistry & Biochemistry > > University of Alaska Fairbanks > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Conor Broderick <cbr...@ma...> > *Sent: *Tuesday, October 27, 2020 2:36 PM > *To: *jmo...@li... > *Subject: *[Jmol-users] Natural Bond Orbital Display Issues > > > > Hi All, > > > > I've been trying to display NBOs in jmol but have run into some issues. > The first thing I tried was downloading the NBO visualization helper > extension ( > http://chemgplus.blogspot.com/2013/08/jmol-nbo-visualization-helper.html), > and while I was able to get the program running when I tried to open a > large molecule (~1200 molecular weight) .nbo file the data section came up > completely blank after pressing the "run" button. I then generated the NBOs > of water, and using the same workflow I got an output in the nbo visualizer > stating "energy data could not be parsed. It is most probably missing in > the .nbo output file." > > > > I'm wondering if anyone else has used this software before and if so you > might have experience troubleshooting it. Regardless, once I realized I > couldn't figure out the NBO viewer, I moved on to trying to do analysis in > jmol itself. This also led to something of a dead end, as when I try to > display any NBOs using "nbo [number]", I get the exact same output as with > the MO command. For example, I went into the .log file I have loaded in > jmol, found the NBO summary and found that the first NBO is a > carbon-phosphorus sigma bond. > > > > I tried to load this first NBO in jmol by calling "nbo 1" in the console, > but it seems to have just spit out the lowest-energy MO isosurface which is > localized on an aromatic ring involving neither the carbon nor > phosphorous indicated by the NBO .log file. Am I misreading the table, or > just calling the command incorrectly? I know that from the jmol > documentation the NBO command is very similar to the MO command but there > is a "type" parameter I do not completely understand, but I had assumed the > NBO command would default to calling the NBO isosurfaces instead of the MOs > with similar labels. > > > > Any advice would be much appreciated -- and in addition thank you to the > folks who have answered the flurry of questions I've sent to the mailing > list the past few days. As an undergrad at a PUI there isn't a huge jmol > knowledge base for me to ask on my faculty and these responses have been > very helpful! > > > > Best, > > > > - Conor > > > > __ > > Conor Broderick | *Macalester College, Chemistry & English ‘21* > > > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |