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Re: [Jmol-users] Natural Bond Orbital Display Issues
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From: John K. <jwk...@al...> - 2020-10-28 00:13:43
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:612.0pt 792.0pt; margin:72.0pt 72.0pt 72.0pt 72.0pt;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal>Hi Connor,</p><p class=MsoNormal>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?</p><p class=MsoNormal>John Keller</p><p class=MsoNormal>Dept of Chemistry & Biochemistry</p><p class=MsoNormal>University of Alaska Fairbanks</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal style='border:none;padding:0cm'><b>From: </b><a href="mailto:cbr...@ma...">Conor Broderick</a><br><b>Sent: </b>Tuesday, October 27, 2020 2:36 PM<br><b>To: </b><a href="mailto:jmo...@li...">jmo...@li...</a><br><b>Subject: </b>[Jmol-users] Natural Bond Orbital Display Issues</p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi All, </p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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 (<a href="http://chemgplus.blogspot.com/2013/08/jmol-nbo-visualization-helper.html" target="_blank">http://chemgplus.blogspot.com/2013/08/jmol-nbo-visualization-helper.html</a>), 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." </p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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.</p><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>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. </p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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! </p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Best,</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>- Conor<span style='color:#888888'><o:p></o:p></span></p><div><div><p class=MsoNormal><span style='color:#888888'><o:p> </o:p></span></p></div></div></div><div><p class=MsoNormal>__</p></div></div><p class=MsoNormal>Conor Broderick | <i>Macalester College, Chemistry & English ‘21</i></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
