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Re: [Jmol-users] Natural Bond Orbital Display Issues
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From: Conor B. <cbr...@ma...> - 2020-10-29 18:37:09
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Hi Dr. Keller, I just tried running your input script, and unfortunately it fails when run in my version of webMO. I checked out the default state of the file for me and it is the following: #N B3LYP/6-31G(d) SP GFINPUT POP=(FULL,NBORead) Geom=Connectivity Acetone_NBO_Test 0 1 C C 1 B1 C 2 B2 1 A1 H 3 B3 2 A2 1 D1 H 3 B4 2 A3 1 D2 H 3 B5 2 A4 1 D3 O 2 B6 1 A5 3 D4 H 1 B7 2 A6 3 D5 H 1 B8 2 A7 3 D6 H 1 B9 2 A8 3 D7 B1 1.540000394 B2 1.540000394 B3 1.090000499 B4 1.089999580 B5 1.089999580 B6 1.275000000 B7 1.090000499 B8 1.089999580 B9 1.089999580 A1 119.9999310 A2 109.4712505 A3 109.4712163 A4 109.4712163 A5 120.0000345 A6 109.4712505 A7 109.4712163 A8 109.4712163 D1 180.0000000 D2 -60.00000517 D3 60.00000517 D4 180.0000000 D5 180.0000000 D6 -60.00000517 D7 60.00000517 1 2 1 8 1 9 1 10 1 2 1 1 7 2 3 1 3 2 1 4 1 5 1 6 1 4 3 1 5 3 1 6 3 1 7 2 2 8 1 1 9 1 1 10 1 1 $NBO FILE=NBODATA AOPNAO=W32 AOPNHO=W34 AOPNBO=W36 DMNAO=W82 DMNHO=W84 DMNBO=W86 FNAO=W92 FNHO=W94 FNBO=W96 ARCHIVE PLOT $END When copying your script and replacing the POP=(FULL, NBO6READ) with POP=(FULL, *NBOREAD*), I was able to get a run to complete, but it again did not generate a .46 file (all other xxx.## files generated fine). At this point I think either I'll need to install a newer version of the NBO software or do the earlier brute forcing attempt, unless there is a command with which I can directly generate the .46 file that is not ARCHIVE or PLOT. best, and thank you for the help - Conor On Wed, Oct 28, 2020 at 11:15 PM John Keller <jwk...@al...> wrote: > Here is what I am doing now. No need to get nbo 7. > > > > ------------- > > #N B3LYP/6-31G(d,p) SP GFINPUT POP=(FULL,NBO6Read) > > > > C3H6O > > > > 0 1 > > C 0.00000000 0.00000000 0.00000000 > > C 0.00000000 -1.33367900 0.77000100 > > C 0.00000000 -2.66735800 0.00000000 > > H 0.00000000 -3.49584500 0.70831500 > > H -0.88998100 -2.72509900 -0.62665700 > > H 0.88998100 -2.72509900 -0.62665700 > > O 0.00000000 -1.33367900 2.04500100 > > H 0.00000000 0.82848700 0.70831500 > > H 0.88998100 0.05774100 -0.62665700 > > H -0.88998100 0.05774100 -0.62665700 > > > > $NBO FILE=NBODATA PLOT ARCHIVE $END > > ------------- > > > > In WebMO Job Manager, Select the job, Download the Job Archive. Expand the > archive on your local machine, then in Jmol: > > > > $ cd <folder containing the job files> > > $ load nbodata.31 > > $ nbo type nbo > > $ nbo 10 > > > > I assume it’s possible to modify the appearance of these surfaces, and > hopefully plot more than one simultaneously. > > John K. > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Conor Broderick <cbr...@ma...> > *Sent: *Wednesday, October 28, 2020 7:42 PM > *To: *Robert Hanson <ha...@st...> > *Cc: *jmo...@li... > *Subject: *Re: [Jmol-users] Natural Bond Orbital Display Issues > > > > Amazing! Thanks for the update. Hopefully this will be the last question > on my end, but do you happen to know the Gaussian command (I am using > Gaussian 16) to output the .46 file? It doesn't seem to generate with > "plot" and "archive," and I tried adding "label" but those runs seemed to > fail immediately. I'm concerned that this may have run up against the > limits of what I can do without getting NBO7. > > > > best, > > > > - COnor > > > > On Wed, Oct 28, 2020 at 9:09 PM Robert Hanson <ha...@st...> wrote: > > (actually, it accesses those files immediately upon loading. > > > > On Wed, Oct 28, 2020 at 10:08 PM Robert Hanson <ha...@st...> wrote: > > Meaning, what we need are these: > > > > > > > * // .31 AO basis // .46 (labels)* > > > > What you do is load one of these: > > > > // .32 PNAO no beta coef > // .33 NAO no beta coef ; adds orbital types > // .34 PNHO alpha+beta > // .35 NHO alpha+beta > // .36 PNBO alpha+beta > // .37 NBO alpha+extra+beta+extra > // .38 PNLMO alpha+beta > // .39 NLMO alpha+extra+beta+extra > // .40 MO alpha+beta > // .41 NO alpha+beta > // .44 PRNBO alpha+beta > // .45 RNBO alpha+beta > > > > And it will automatically access the .31 and .46 files when you then issue > the NBO command. Or you can load the .31 file and then use > > > > NBO TYPE NLMO > > > > or similar command, then > > > > NBO 10 > > > > Bob > > > > -- > > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We > honor with gratitude the people who have stewarded the land throughout the > generations and their ongoing contributions to this region. We acknowledge > the ongoing injustices that we have committed against the Dakota Nation, > and we wish to interrupt this legacy, beginning with acts of healing and > honest storytelling about this place.* > > > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
