Natural Bond Orbitals (NBO) visualization

This is the second post on a series which will try to address common technical questions in computational chemistry that recursively appear on the CCL.

The Natural Bond Orbitals analysis is a powerful tool in population analysis calculations which is more robust than the traditional Mulliken approach, if for no better reason because its almost insensitive to the change of basis set while Mulliken’s P.A. is highly sensitive to basis set effects. Another advantage of the NBO analysis is that it provides a localized depiction of the electron density over a molecule, making it more related to chemists intuition. So far I have only worked with Gaussian 98, Gaussian 03 and only recently with Gaussian 09 in calculating NBO’s although it is possible also to perform them with GAMESS and the standalone NBO5.0 program created by Frank Weinhold. Visualizing them, however is never a straightforward process, and quite often we see more questions on the CCL than answers trying to address the matter. Most of the answers are concerned with what visualization programs to use but they seldom provide step by step instructions, furthermore most manuals are a bit cryptic about the procedure to plot this orbitals.

In Molekel 4.3

Make sure that the route section in your input file includes the following options: pop=nboread; gfoldprint (in case you are using G03 or even G09) or gfprint (in case you are still running G98), e.g.:

#P opt rhf/6-31G(d,p) pop=(full,nboread) gfoldprint geom=connectivity

This calculation requests a geometry optimization followed by a Natural Bond Orbital population analysis (with keywords to be read) using the Restricted Hartree-Fock method with the split valence basis set 6-31G(d,p)

NOTE: I have my own issues and concerns about the use of DFT along with NBO but maybe that will be treated in another post.

At the end of the input file, after the infamous blank line type the following:


You may include other keywords such as BNDIDX which generates a Wiberg bond index (order) matrix; or BOAO which generates the same matrix but in the Natural Atomic Orbitals basis. The PLOT option will generate a series of files with numerical extensions. The one you want to pay attention to is filename.47

If you are using Gaussian 03 or Gaussian 09 and STILL want to use Molekel 4.3 then you probably already know you have to change 03 for 98 on the header of the output file:

****************…              ****************
Gaussian 03:  x86…  –>       Gaussian 98:  x86-
2-Feb-2009                               2-Feb-2009
***************…                ****************

That aside, load your output file (filename.out or filename.log) on Molekel 4.3 as usual. Then go to Load -> nbo orb and load filename.47. Now, go to Compute -> Orbital and now select the Natural Bond Orbital you are interested in. This should do it! As an interesting exercise try computing the same orbitals (lets say HOMO and HOMO-1) with and without loading filename.47 in order to observe the difference between the shape of the MO’s and NBO’s. Molekel 4.3, though, is filled with bugs that will make it close unexpectedly, specially when running under Windows Vista. Sometimes the window closes because some sort of resolution problem, specially when taking snapshots (interestingly enough this happened to me when the background color was set to white) decrease the resolution of your monitor before taking the snapshot to prevent this problem. Some people complain about the look and feel of the latest molekel version so they stick to this old bugged one, so that is why I’m posting this method.

In Gasusview 3.0

This is the gaussview version I currently work with. When performing the NBO analysis on Gaussian (by the way, Gaussian 09 cannot be visualized with gaussview 3.x) use the savenbo option in the rout section, for example:

#P opt HF/6-31G(d) freq=noraman pop=(ful,nboread,savenbo) geom=connectivity

This will save the NBO coefficients into the checkpoint file. Load the output file with gaussview normally and then click on the Molecular Orbital icon (or go to Edit -> MO’s). This will open a new window with four tabs at the bottom of the molecule image. Click on the ‘New’ tab and load your checkpoint file. Gaussview will automatically format the chk file (this can cause some troubles when crossing architectures or platforms, so be careful to generate the proper formatted chk file!) Once load select the orbital you need to visualize and go to the ‘Visualize’ tab and click update; the orbital displayed is the Natural Bond Orbital. In this tab you can also adjust certain parameters like the isovalue (which is set to 0.02 by default) or the cube grid which controls how smooth the surface looks. UPDATE: According to John Keller from Alaska you can use this methodology when calculating with G09 and using Gview3.x, this also allows to visualize vibrations when this same software combination is used.

As usual, this post will be updated whenever I find some more useful information about the matter. Rate this post or leave a comment, just to know if you found it useful. Thanks!


About joaquinbarroso

Computational and theoretical chemist in his early forties, in love with life, science, baseball, and literature. Science literacy makes us responsible citizens, it is therefore a scientific duty to talk, write, and engage with the general public; as Feynman said, if you find science boring, your learning from the wrong teacher. "Make like a molecule and react!"

Posted on September 24, 2009, in Computational Chemistry, Gaussian, NBO, White papers and tagged , , . Bookmark the permalink. 154 Comments.

  1. With regards to viewing NBOs. I use ChemCraft as my visualization program. It renders all the orbitals for me and I can select which orbitals to render. However I am at a loss when it comes to determining which ones I should be looking at and what they mean exactly. There are two types that I can see: populated and unpopulated. Any insight as to how the NBOs are broken down, what to use certain ones for, and anything else along those lines?? I’d love to use this tool but have no idea where to begin (guess I just don’t understand the mechanics behind how Gaussian outputs these).


    • Hi Eric, this was a long due reply. Check the other post on NBO in this same blog for a bit more info on NBOs. In a nutshell, NBOs are a localized (in the Lewis sense) representation of MOs, you take them and re-orthonormalize them to get NBOs. This eliminates some basis set dependencies on properties coming from the population analysis (like charges for instance, Mulliken charges from MO pop analysis are strongly basis set dependent).
      NBOs are divided into CR (core), BD (bonding), LP (lone pairs), RY (Rydberg orbitals, somewhat the analog of virtual orbitals of the SCF) and BD* (antibonding).
      Take also a look at the NBO5.0 home website for more details and a helpful pdf manual.

      Thanks for reading!

  2. Thanks for the quick reply. I should be more specific in my question. I do not know if you are familiar with “ChemCraft” but its underlying mechanics are the same as any other visualization program as it draws its information directly from output files from programs such as Gaussian. I should note that I’ve been trying to do my own internet research on the topic and I have found some halfway decent sites that discuss this but in a more cryptic tone. If you have any future posts about this topic I will gladly wait for them otherwise let me know if you are interested and I will shoot some questions your way.

    Again keep up the good work. Your blog has been most helpful in numerous situations!

  3. Estimado Dr. He realizado todos los pasos que comenta respecto a Molekel y no me aparece el fichero filename.47 (sólo salen del 31 al 41). ¿Sabría cuál es el motivo? ¿Es necesario el keyword geom=connectivity?

    Muchas gracias.

    • Hola
      El keyword geom=connectivity no tiene nada que ver, no es por ahi. Intenta utilizar el keyword ARCHIVE=filename en la seccion de opciones de NBO (usando pop=NBORead en el route section). Asimismo puedes intentar con la opcion PLOT en la misma seccion.


  4. Estimado Dr. Respecto al uso de Gausview, también sigo sus sugerencias, sin embargo, al final del trabajo me aparece el mensaje de error “NBStor is confused about NOcc.” ¿Me podría decir algo al respecto?
    Por cierto, estoy trabajando al nivel CASSCF.

    • El error que comentas esta asociado a una ocupacion anomala de los NBOs (los numeros de ocupacion no corresponden al orden energetico de los mismos). Al estar usando un nivel como CASSCF es posible que la mezcla de estados deslocalize fuertemente la densidad electronica y al renormalizar la base obtienes orbitales semivacios con baja energia.
      Voy a estudiarlo durante el fin de semana y la proxima posteo algo al respecto, ok?

      Gracias por escribir!

      FOR NON SPANISH SPEAKERS: The state mixing in CASSCF might be strongly delocalizing the electronic density which results in bogus occupation numbers related to their energy levels. More to come on this topic next week 😉

      • Dear joaquinbarroso,
        During running a job to calculate NBO using pop=(NBO, savemixed), I faced this error message:
        Sorting of NBOs: 1080 1049 1074 1043 1078 1047 784 783 1079 1048
        Sorting of NBOs: 1069 1038 1073 1042 629 668 499 460 655 642
        Sorting of NBOs: 278 317 473 486 304 291 733 577 694 616
        Sorting of NBOs: 590 720 564 421 239 369 343 265 382 226
        Sorting of NBOs: 525 447 551 408 252 356 707 603 434 538
        Sorting of NBOs: 395 213 1087 1056 1081 1050 1075 1044 772 759
        Sorting of NBOs: 678 329 510 746 1040 1071 1053 1084 1077 1046
        NBStor is confused about NOcc.
        Error termination via Lnk1e in xxxx/g03/l607.exe at Mon Aug 9 12:35:56 2010.
        Job cpu time: 0 days 3 hours 25 minutes 11.0 seconds.

        Could you help me please how I could solve this problem.
        Best regards,

      • Dear Moro
        As you already read this has to do with a warning that NBO sends you if the occupation of each orbital doesn’t follow the aufbau principle, i.e., the energy and the population don’t follow the same order. Try the following:
        1) Make sure you are working with a minimum of the PES by performing a vibrational frequency analysis (you probably already did but its better to be sure)
        2) Change your basis set. Although NBO is not so sensitive to change in basis set there could be a reorthonormalization problem with the particular one you are using.

        If I come across another tip I will let you know, in the mean time try the above and let me know how it went. Best wishes!

  5. snehasis banerjee

    Dear Sir
    How can i get Molekel 4.3? this site now giving v5.4. and i am not able to draw nbo plot in this version.
    please help.

  6. This message if for snehasis banerjee: Try to draw nbo plot with chemcraft.

  7. Estimado Dr.

    Perdón por haber usado este blog para responder a snehasis, pero es que yo tampoco puedo ver los NBO plots con molekel 5.4 y parece que con chemcraft sí se puede (dando los mismos pasos que Ud. me dijo para molekel, excepto la indicación gfoldprint).

    Por cierto, le escribo para pedirle de nuevo ayuda:
    No consigo ver los “Natural Bond Order” ni “Second Order Pertubation Theory Analysis…” con NBO 3.0 ¿Tengo que poner alguna instrucción en la línea $NBO $END?

    Muchísimas gracias.
    PD: ¿Cuando regresa a Europa?

    • Hola de nuevo!
      Me parece perfecto que le hayas contestado a Snehasis, no hay por que pedir perdon! Y por favor, llamame Joaquin simplemente.
      No tengo experiencia con Chemcraft, lo voy a bajar para darle un vistazo pero por lo que me escribes parece que es bastante similar a Molekel 4.x, la version 5.4 de Molekel nunca me gusto y preferi seguir usando la anterior junto con Gaussview. Voy a ver como se hace con Molekel 5.0 y lo posteamos para la proxima.
      Sobre tus preguntas: Revisa el otro post sobre NBO en este mismo blog (categoria NBO o white papers) ahi hay algo al respecto. Me extrania que no veas el ‘2nd order pert analysis’ por default. Utiliza los keywords: E2PERT y BOAO (Bond Order in the Atomic Basis set) en la linea $NBO $END Igualmente puedes utilizar la instruccion BNDIDX para obtener los ordenes de enlace de Wiberg.

      Me da mucho gusto saber que el blog esta sirviendo de ayuda. Regreso a Europa en Enero o Febrero a mas tardar, concretamente a Hungria (Pecs de nueva cuenta).


  8. Perdón, quería decir Gaussian NBO version 3.1

  9. snehasis banerjee

    I have received the file sent by you. Thanks a lot sir for your help.

  10. snehasis banerjee

    Now i can draw the my relevant plot. But sir the background is always black. how to change it to white.
    please help

    • Right click on working area, select Color menu, set all RGB values to 1.0 and then click on apply to background top and background bottom. Never use the [x] buttons to close dialog windows! it will cause the program to crash! instead always use the Cancel button at the bottom of it.

  11. snehasis banerjee

    Thanks a lot sir. Now everything is fine. I have a new question. Is it possible to visualize NBO-NBO transition by Molekel?

    • I’m not sure what you mean by NBO-NBO transition, could you tell me more about what you are trying to do? However I’m pretty sure Molekel cannot visualize transitions of any kind but maybe I’m not understanding what you want to do.
      Give me more information so I can help you better.

  12. Hola Joaquín (por cierto, mi director de tesis también se llama Joaquín),

    ¿Me podrías enviar el molekel 4.3 (o decirme dónde conseguirlo para compararlo con chemcraft?

    Otra preguntilla:
    ¿Cómo son de fiables los órdenes de enlace de Wiberg?

    Muchas, muchas gracias.

    • Hola!
      Te he enviado los archivos que me solicitas. Sobre los indices de Wiberg, considero que son muy confiables en cuanto a que son poco dependientes de la base utilizada, sin embargo como cualquier otro orden de enlace debe ser tomado de manera relativa, es decir, toma un enlace que tu sepas esta bien definido en tu molecular como enlace sencillo y observa que orden presenta (seguro no sera 1, sino 0.85 o 1.15 etc.) y en base a este compara los demas. Haz el ejercicio de calcular los ordenes de enlace para el acido acetico (tanto wiberg como mulliken) a diferentes niveles de teoria (HF/STO-3G; HF/3-21G**; HF/6-31G…) y compara los valores obtenidos.
      Los ordenes de enlace de Wiberg son calculados con el keyword BNDIDX en la seccion $NBO … $END, claro que en el route section debes incluir pop=(NBORead)


  13. snehasis banerjee

    Dear sir,

    Thanks a lot for your reply. Actually i mean transition from any partcular nbo to another nbo can be visualized or not.
    Ref: Chem. Eur. J. 2008, 14, 731–740 ( Fig 4c)
    Please help me sir.

    • Dear sir,

      I am in the same problem since last two years. Please help me to suggest is it possible to draw a plot where both donor as well as acceptor orbital can be drawn. part of one of my output result is showing:

      Threshold for printing: 0.50 kcal/mol
      E(2) E(j)-E(i) F(i,j)
      Donor NBO (i) Acceptor NBO (j) kcal/mol a.u. a.u.
      80. LP ( 2)Cl 22 / 75. LP*( 5)Pt 1 20.74 0.52 0.018
      I can draw NBO 80 and NBO 75 but is it possible to draw 80+75 in a single diagram so that one can easily understand how the donor-acceptor orbital looks.
      As a reference: Chem. Eur. J. 2008, 14, 731–740 ( Fig 4c)
      please help if i am able to express my problem clearly.
      Thanks and regards

  14. Senor Joaquin, estoy intentando generar el file.47 y luego usarlo para encontrar los canoncal molecular orbitals… estructura ya esta optimizada…
    Mi input dice asi…
    # b3lyp/tzvp geom=connectivity pop=nboread

    $NBO archive file=f8omecmo $end

    Pero siempre obtengo el mismo error ” WANTED AN INTEGER AS INPUT.
    $NBO archive file=f8omecmo $end ”
    Podrias por favor ayudarme?
    Mil gracias

    • el problema que mencione arriba a sido solucionado, pero ahora que genere el file.47 del pop=nboread….no se como calcular los canonical molecular orbitals, podrians explicarme como?

      • Me da gusto saber que resolviste el problema anterior 🙂
        Los orbitales canonicos son aquellos que se obtienen de la solucion del campo autoconsistente SCF por medio del metodo de Hartree-Fock, por lo que el metodo NBO no es el que los calcula. En otras palabras tu archivo de salida ya contiene los orbitales canonicos una vez que converge, no requieren de ser calculados a posteriori. Carga el archivo de salida con Molekel o Gaussview y selecciona las opciones correspondientes a la generacion de MO’s.
        Si necesitas mas ayuda no dudes en contactarme, con mucho gusto resuelvo tus dudas.

  15. Baje de la internet el Molekel, v…abro el archivo .log sin problema, sin embargo no encuentro el Load -> nbo orb, para cargar el archivo .47, por lo tanto no he podido ver los canonical molecular orbitals. Me podrias ayudar con eso? Mil gracias de antemano. por otro lado soy como principiante en todo esto y si pudieras darme de una manera solo un poco mas detallada (nada que te quite mucho tiempo) que es exactamente un canonical molecular orbital (tengo ordenes de mostrar estos orbitales, pero la verdad no estoy seguro que son exactamente). necesito visualizarlos, pero aun no he podido, mil gracias.

    • Hola de nuevo, Henry

      Los canonical MO’s no vienen del análisis NBO sino del SCF. Búscate el libro Quantum Chemistry de Ira N. Levine o el de D. McQuarrie para una explicación más amplia. No he trabajado mucho con la nueva versión de Molekel pero la próxima semana te daré más información sobre como usarlo. Por lo pronto, si lo que necesitas es mostrar los Canonical MO’s busca la opcion calculate -> orbital, te va a preguntar si quieres usar los coeficientes del SCF o los valores propios de la matriz de densidad, escoge los primeros y selecciona el orbital que quieras mostrar. Supongo que tu tarea es mostrar los orbitales HOMO y LUMO (ejercicio clásico), estos los puedes reconocer por su ocupación ya que, por definición, HOMO es el último orbital ocupado y el LUMO es el primer desocupado. Espero que te sirva esta información, de cualquier manera la próxima semana ahondaré más al respecto.


  16. Hallo Joaquin Barroso,

    you said “Gaussian 09 cannot be visualized with gaussview 3.x”. Do you have any idea, how to visualize or extract vibrational data obtained by Gaussian 09 with Gaussview 3?

    Thank you 🙂


    • Hi Yvonne

      Indeed I found that NBO results from G09 calculations cannot be visualized in the standard way with GaussView 3.x. If you want to visualize any other results, such as Molecular Orbitals, vibrations, etc. you can use GV 3.x without a problem.
      I would need more information about your problem and needs to help you in a better way. In the mean time, if you only want to visualize the G09 calculated vibrational frequencies (or just list them along a simmulated spectrum) you can use GV 3.x

      Thanks for reading!

      • Hey Joaquin,

        I just tried one frequencie-calculation with gaussian09, and when I try to open the corresponding log-file with gaussview 3.09 an error message occures saying “CConnectionGLOG::Parse_GLOG() Failure reading vibrational data. Last line read=…”. Perhaps this file is just corrupted. I’ll try a new calculation.
        Thank you nevertheless!

        greetings 🙂

      • Hi Yvonne

        I’m terribly sorry for the delay of my reply.
        Your file is not corrupted, it just didnt finish! you have to open the log or out file and read the final lines to realize what the error was and act accordingly. You probably ran out of memory but I would need to know what the error is (also what method and level of theory you employed) in order to give you a precise set of instructions for fixing it.

        Please let me know if you got this message

        Best wishes

      • Hey Joaquin,

        The log file says, it finished properly by the typical last line: “Normal termination…”. So if you send me an email, I could send you the log file just for throwing a glance on it?

      • Hi again Ivonne!
        I hope you get this answer straight into your inbox, otherwise I dont know if you’ll see it. I found out that in order to visualize vibrations on GV3.x from a G09 calculation you have to change the lines saying “Atom AN” to “Atom AN”. The first one has TWO spaces between both words, while the second has only ONE and this is the way to go. I found this out by chance on the CCL, check the following link to a post by Jean Poully, to whom credit is due!

        Danke und Auf wiedersehen!

  17. MiguelRamírez

    Estimado Joaquin:

    Estoy analizando unos compuestos organometálicos con en GENNBO 5.0. Observo resultados diferentes a los que da el Gaussian 09W, que utiliza el NBO 3.1. El problema que se me plantea es que no sé cómo visualizar estos orbitales, pues todos los métodos citados hacen uso de un fichero calculado con Gaussian,que me mostrarían los orbitales “incorrectos”. ¿Existe algún programa que lea los ficheros .nbo?. Gracias por tu blog.

    • Estimado Miguel

      Disculpa la demora de mi respuesta.
      Los ficheros .nbo son leidos directamente con el programa NBOView provisto por los mismos autores de GENNBO5.0 (Frank Weinhold y compañía). No estoy seguro a que fichero de Gaussian te refieres ni a porque les llamas incorrectos. El procedimiento descrito en este post debiera permitirte visualizar los orbitales en cuestión si es que los has salvado en el fichero .chk o en el fichero de salida (.out o .log). Por favor dame más detalles para poder ayudarte mejor.

      Gracias y saludos

      • Miguel Ramírez

        Gracias Joaquin.

        No se si mi problema se debe a que la versión del NBOView que he probado es la 1.0 pero cuando intento dar como input el archivo.nbo me replica el programa que no encuentra los archivos .31 a .46. Estos los genera, aparentemente el Gaussian (con su NBO 3.0) y, que yo sepa, no el propio GENNBO (NBO 5.0), con lo que la visión de los orbitales sería la de los generados con la vieja versión NBO. ¿Qué hago mal?.

        Gracias, nuevamente, por tu magnífico blog

        Miguel A. Ramírez

      • Estimado Miguel

        Si lo que necesitas son los archivos .31 a .46 intnenta usar la opción PLOT en la sección $NBO, si necesitaras el archivo .47 entonces utiliza la opcion ARCHIVE=filename (sin extensión) en la misma sección. Esto debería ayudarte a obtener los archivos que te pide NBOView.

        Déjame saber como te fue, ¿ok?


  18. Estimado Joaquín:
    Antes que nada quisiera disculparme si mis consultas son muy basicas,soy nueva en los esudios de química computacional y leyendo su blog me doy cuenta que me queda muuuucho por aprender. Mi consulta es la siguiente: he optimizado unas estructuras con gaussian 03 a las que les quiero hacer MEP, y el programa para visualizarlo que tengo es el molekel 4.1. El problema es que no me deja crear la superficie, le he cambiado el 03 por 98 en el .out pero sigo sin poder lograrlo. Usted podrá ayudarme?

    • Estimada Yami

      Antes que nada, perdona la demora de mi respuesta. Para hacer lo que estás intentando es necesario hacer que G03 imprima la base (3-21G**; 6-311+G, etc.) en el archivo de salida. Esto lo logras utilizando la instrucción GFOLDPRINT en el route section de tu optimización. Existen otras palabras clave como GFINPUT y GFPRINT pero para que Molekel 4.x la pueda leer necesitas el estilo antiguo de Gaussian (de ahi gfOLDprint :D) Esta instrucción te debe permitir generar la superficie.
      Nunca te preocupes si tus preguntas son muy básicas, eso no las hace menos válidas. Por favor ponte en contacto para saber que leiste esta respuesta y saber si te fue de ayuda.


  19. I tried to run a Gaussian03 file with the keywords you requested (pop=nboread gfoldprint and $NBO PLOT $END at the end), and got a serie of .31-.41 files but not the .47 file. How can I obtain this file? And can Molekel open .31-.41 files?

    • Dear Grigoriy:

      You are right! PLOT will only generate those files you mentioned. Try using the jobname.37 file instead. Nonetheless there is another way to generate file .47 which is by using the ARCHIVE=jobname in the $NBO section. This will generate jobname.47

      Sorry about the delay of my answer, but I was on vacations 🙂
      I hope this helps, please let me know how it went, ok?
      Best regards

      • I found that after opening an output file in Molekel 4.3, either .37 or .47 files can be opened (but they should be renamed to .orb files). However, at my computer, after choosing “Compute -> Orbital” and selecting the orbital, the program shows a file browser for opening a .macu file. I didn’t find this file so I was unable to render a NBO or a MO.
        To obtain the .47 file, at my computer ARCHIVE should be specified in the $NBO section (not ARCHIVE=jobname as you suggested).

      • That file browser is actually asking you to create a .MACU file. Give it a name and then it should generate the surface, if it doesn’t then go to SURFACE (right click menu on main interface) which will open a window: on the top click on LOAD (macu being selected below it), browse for your recently created macu file and then click on “create surface” (on the SURFACE window). Since what you are trying to display are orbitals, make sure the “both signs” option is enabled. I think the cutoff value is displayed as 0.02 by default but maybe it stays at zero (I’m not sure right now) you can play with it of course.
        You are right, using ARCHIVE=jobname only names the files but its not necessary to generate them.
        Sorry for the lateness of my response.

  20. Estimado Joaquin:
    Muchas gracias por haber respondido. He intentado hacer las superficies esta vez colocando gfoldprint en mi comando, pero no las puedo realizar. No se si se puede probar otra palabra clave o si voy a tener que conseguir G98 u otro molekel (lo cual no es tan fácil)para poder representarlas. Por otro lado, no se si estas consultas las tengo que colocar en otra parte del blog o está bien seguir escribiéndolas aquí. Bueno espero tu respuesta. Gracias! y Saludos!

    • Estimada Yami
      Entiendo que realizas optimizaciones de geometría con G03, utilizas la opción gfoldprint dentro del archivo de entrada en el route section (# opt metodo/base gfoldprint ….) es correcto?
      Con Molekel 4.3 (si no lo tienes te lo envío porque parece que tienes el 4.1, el cual no conozco) cambias el G03 por G98 para que la molecula no salga plana; la cargas en molekel, luego con el click derecho sobre la pantalla te vas a COMPUTE -> EL. DENSITY (o MEP en tu caso). Te va a pedir un nombre para el archivo .MACU a generar así como una ubicación para guardarlo. Esto debiera ser suficiente para poder generar la superficie deseada. Cualquier otra información házmelo saber y con gusto te ayudo.


  21. Hey Joaquin, did you solve Yvonne’s problem above? I get the same problem. I run my data using Gaussian 09 and my file says it terminated normally and all my data converged. There are numbers under my vibrational frequencies in my log file but I cant see them in gaussview. Any idea what Im doing run or what to do to fix them?

  22. Dear Dr. Barroso,
    Very nice blog on NBOs. I am able to visualize MOs or NBOs from the Gaussian09 .fchk file using GV 3.09 on various XP and Win7 systems. Just put “formcheck” in the route card. G09 vibrations can also be visualized from the .fchk output file.
    Best Regards from Alaska!
    John K.

    • Hi John!
      Thanks for your nice words and tips! Let me see if I understand: You can alternatively switch between MOs and NBOs with GView when using the fchk file? do you have to save the NBOs in the chk file somehow (i.e. do you use savenbo)?
      I will update the corresponding posts with your tips and will give you full credit for them of course.

      Best wishes from Mexico City!

      PS I’ve always wanted to go to Alaska! Two years ago I almost convince some friends to drive all the way up there but in the end we couldn’t, maybe someday.

  23. Estimado Dr. estoy intentando realizar unos calculos para encontrar los estados excitados de cierta molécula y tengo entendido que se puede hacer con CIS y con TD-DFT pero resulta que cuando voy a optimizar la molécula en TD-DFT con PBE1PBE/6-31g* y me resulta el siguiente error



    Con el CIS me resulta el error de l9999 pero ya lo estoy tratando de solucionar igual cualquier ayuda se lo agradeceria.

    Muchas gracias y espero que pueda ayudarme

    • Hola Diana

      l9999 no es un mensaje de error, es uno de los tantos programas (links) de Gaussian, de hecho es el que termina el trabajo, imprime la cita y te imprime cuanto tardó. Me gustaría ver tu archivo de entrada para poder ayudarte mejor. He visto ese error (ERROR IN INITNF…), intenta cambiar el conjunto de coordenadas, ya sea de cartesianas a matriz Z o visceversa dependiendo cual sea tu caso y házme saber como te fue.

      Espero que mi respuesta no sea ya anacrónica

  24. Hola Dr. le cuento que ya pude realizar los calculos ensayando lo de la matriz que usted me dijo anteriormente y le agradezco muchisimo.

    Ahora lo que quería es hacerle un pregunta, lo que pasa es que quiero realizar unos calculos en solucion pero con TD-PBE1PBE y CIS para obtener los estados exitados de la molecula en cierto solvente, será posible que usted me indique como hacerlo, tengo entendito que hacen con PMC,pero hice algunos preliminares utilizando estos keywords hf/6-31g(d,p) scrf=(pcm) opt=tight nosymm td-pbe1pbe
    pero obtengo este error

    United Atom Topological Model (UA0 parameters set).
    UA0: Hydrogen 2 is unbound. Keep it explicit at all point on the
    UA0: potential energy surface to get meaningful results.
    Error termination via Lnk1e in C:\G03W\l301.exe at Tue Nov 02 10:43:32 2010.
    Job cpu time: 0 days 0 hours 6 minutes 18.0 seconds.

    Le agradeceria mucho su ayuda y de antemano muchas gracias por lo anterior

    • Hola Diana

      La respuesta a tu pregunta estoy seguro que se encuentra en el cuerpo de este post que escribí sobre PCM
      Pero para ser precisos el problema que tienes es con la definicion de la cavidad. Gaussian asigna una esfera a cada átomo (o grupo de atomos como con el modelo UA0 que es el default) y en tu caso un atomo de H quedo fuera de la superficie imaginaria que define como cavidad. Utiliza SCRF=(PCM,Read) y al final del input deja una linea en blanco y bajo ella escribe
      puede ser Bondi, Pauling, UAKS, etc. te recomiendo ver la siguiente pagina de Gaussian
      También sugiero escribas bajo el modelo lo siguiente:
      –linea en blanco–
      Espero que te sirva


  25. Dear Dr. Barroso,
    I’ve been trying to run a job with an NBO deletion followed by opt using B3LYP (more specifically: #p B3LYP/6-311++G(d,p) NOSYMM POP=NBODel OPT scrf=(solven=water,pcm)). But I am getting the following error message:


    Error termination via Lnk1e in /usr/local//g03/l114.exe at Wed Dec 1 00:29:48 2010.

    The same job will terminate normally with #N HF/6-31G(d) NOSYMM POP=NBODel OPT.
    I know that you said it is best to use HF but is there a way to calculate these in B3LYP with the 6-311++G(d,p) basis set or would you just strongly suggest against it?

    Any advice would be much appreciated!
    Thank you,

    • Hi Jean
      Sorry for the delay in my reply.
      Using B3LYP with NBO is not wrong, and I’m not adamant against it, let’s just say I frown upon it. Anyway, your error here is very curious. Have you tried to run your same job without the SCRF part? Maybe you can do that and then re-optimize it with SCRF.
      If this error comes within the NBODel section then I’m afraid your deletion generated a Hessian matrix that cannot be diagonalized.
      I will take a better look into it if you send me your input and output files.

      Have a nice day!

  26. Leonardo Gómez

    Doctor Barroso:

    Estoy interesado en hacer cálculos de optimización para una nanopartícula de Pd (en fase condensada) de 13 átomos, utilizando hf/lanl2dz en Gaussian 03. Mi pregunta es si usted podría recomendarnos algunas consideraciones para tener en cuenta con estos sistemas ya q

  27. Leonardo Gómez

    Doctor Barroso:

    Estoy interesado en hacer cálculos de minimización de energía para una nanopartícula de Pd (en fase condensada) de 13 átomos en forma de icosaedro, utilizando hf/lanl2dz en Gaussian 03. Mi pregunta es si usted podría recomendarnos algunas consideraciones para tener en cuenta con estos sistemas, ya que los cálculos están tomando demasiado tiempo y en ocasiones se alcanza el número máximo de iteraciones sin obtener resultados.

    De antemano agradezco su pronta respuesta.

    Leonardo Gómez

    • Hola Leonardo!
      Entiendo por lo que están pasando. Mucho depende de las capacidades de cómputo que tengan, aun cuando están utilizando pseudopotenciales full-core. A reserva de que me informes con que recursos computacionales cuentan te doy los siguientes consejos:
      1.- Pre-optimiza a niveles de teoría bajos. Incluso de ser posible utilizando métodos semiempíricos (supongo que en su caso una base pequeña puede ser suficiente bajo el método de HF). La estructura resultante la puedes tratar entonces con tu nivel de teoría seleccionado.
      2.- Los clusters metálicos usualmente tienen alta simetría. Construyan las estructuras en base a los grupos puntuales correspondientes (si es que no están obteniendolas de datos de difracción de rayos x por ejemplo)
      3.- Una vez que tienes un sistema simétrico restringe la función de onda al grupo puntual correspondiente con las opciones symm=(follow,pg=”grupo”) donde “grupo” debe ser reemplazado por tu grupo puntual.
      4.- A veces a gaussian le cuesta trabajo ubicar los elementos de simetría durante rotaciones, intenta orientar el eje de simetria principal sobre el eje z (lamentablemente esta parte sí requiere un poco de ensayo y error)

      Espero que te sirva esta información. Gracias por leerme!

  28. Doctor Barroso,

    Muchas gracias por sus consejos para los cálculos con nanopartículas metálicas de 13 átomos. Le escribo porque estoy tratando de crear un archivo cube en Gaussian y he encontrado que usando el keyword Cube Density se obtienen, pero aunque el cálculo comienza normalmente no termina bien, al final sale:

    ” Evaluate density.
    Using the total density.
    Map the density over a grid of points, CutOff= 1.00D-06
    Writing cube to file .
    IGUnit= -31 Origin= -8.159500 -8.159500 -8.159500
    N1= 80 XYZInc= 0.206570 0.000000 0.000000
    N2= 80 XYZInc= 0.000000 0.206570 0.000000
    N3= 80 XYZInc= 0.000000 0.000000 0.206570
    PGFIO-F-217/formatted read/unit=5/attempt to read past end of file.
    File name = /tmp1/giftex/gaussian25338/Gau-25380.inp formatted, sequential access record = 23
    In source file dencub.f, at line number 541
    Command exited with non-zero status 1″

    También intenté con cubegen, pero no me da resultado.

    Podría indicarme cómo crear archivos tipo cube en Gaussian, le estaría muy agradecido.


    Leonardo Gómez

    • Hola Leonardo

      Mil perdones por la tardanza de mi respuesta.
      Si estas utilizando G09, la respuesta es que el keyword cube ya no es válido, tienes que usar la utilidad cubegen desde la línea de comandos. La sintaxis es la que sigue:

      %>cubegen ‘tipo’ ‘filename.fchk’ ‘filename.cube’

      Este es el estándar, hay algunos parámetros que se pueden modificar como el número de puntos en el cube pero para moléculas “normales” este default debiera bastar.

      En ‘tipo’ se define que tipo de cube quieres (ver tipos disponibles aqui). Es muy importante que hayas formateado tu archivo chk a formatted chk (*.fchk). Ve como usar la utilidad formchk. Finalmente dale un nombre a tu cube file y debieras estar listo. Por favor déjame saber como te fue.

      Saludos y muchas gracias por leer el blog!

  29. Muy buenas, enhorabuena por este blog. Me gustaría hacer la siguiente consulta, cabría posibilidad de obtener molekel 4.3 para ver los NBO, aunque chemcraft los visualiza, quisiera disponer de esa versión también, muchas gracias.

  30. Muy buenas Joaquin, le escribí un mail agradeciéndole la ayuda prestada, espero que lo recibiera. Le animo puesto que este blog está muy bien y sirve de ayuda a muchas personas, reciba un cordial saludo

  31. Sr Joaquin es posible que me pasara molekel 4.3 porque no lo encuentro por ninguna parte y la actual parece que tiene problemas de compatibildad con window.

  32. Bhaskar Mondal

    Dear Dr. Barroso,
    I am Bhaskar Mondal, a research associate at the University of Strathclyde, Glasgow.
    I want to use the standalone NBO 5.0 program. I have the FILE.47 in my hand with the ENABLE.F created gennbo.f program. I want generate the PLOT files using the standalone NBO program. Please suggest me how can I go properly so that I can generate my required nbo output using the standalone NBO program.

    With bets regards,
    Bhaskar Mondal

  33. Manuel Carignan

    Estimado Joaquín:
    La razón por la que me dirijo a usted se reduce a la siguiente consulta:
    Estoy trabajando con un sistema del cual debo adquirir los órdenes de enlace y las longitudes de estos mediante NRT. Para ello le he expecificado al Gaussian 03 el siguiente input:
    b3lyp/6-31+g(d,p) pop=nboread (la molécula ya esta optimizada) y el la línea final luego de la matriz Z las siguientes keywords:
    Creí que expecificando NRT obtendría estos pero por lo visto estaba equivocado.
    Lo único que pude ver al respecto es que es necesario introducir a continuación lo siguiente:
    ¿Es necesario alguna keyword adiconal más?
    Desde ya muchas gracias.

  34. santanu panda

    Hi…….I was using Gaussian 09 to run a frequency calculation. I got an error message ConnectinG::Parse _GLOG() Failure reading vibrational data
    I could not see the vibrational data. My input file is like this…
    # b3lyp/6-31g OPT FREQ nosymm

    • Hi Santanu

      I’m afraid I don’t have an answer for this although I’m pretty sure I’ve seen it before. Please contact the Gaussian tech support at their website. They usually reply very fast!

      Sorry this time. Thanks for reading!

  35. Halo Dr Barroso!

    I would be very happy to learn from you the use of Molekel 5.4. It is bringing me some troubles in visualizing orbitals. I used to work with the 4.3 version but things alot now. Just provide me exact use of “Grid data” and “electron density”. According the the “help” item, I am not getting what I was supposed to get!

    Thanks ahead!

    • Hello Dr. Gahugu

      You have a very interesting name for me. I imagine you live in a beautiful exotic land and probably think the same about me when you read “Barroso” which I find very funny.
      I am afraid I’m not familiar with Molekel 5.4. I still use the old 4.3 version since I don’t like to waste too much time in getting spectacular images when I can just use an informative image to depict what i hope are spectacular numbers! (more science less art; thats my motto) Unfortunately journal publishers don’t seem to agree with me and they are forcing me to switch to others. I hear chimera is great and also vmd; I use gaussview because it’s there and yields acceptable images.

      Thanks for reading!

  36. Hi,
    I have run GAMESS with gmsnbo.src, and I have got .31-.41 files for visualization NBOs. How can I use MOLEKEL to see the outputs of Gamess.

    • I have spent past 3 days tryying to do this, and i found out that easyest way to do that is do it with Chemcraft – simply click open and select .31 file. You can download trial version (150days) or buy it …
      Problem Molekel is that for some reason in new version it is not possible vo view NBOs – they made it on purpose. If you want to use molekel you would need to make a ltle hack – somehow exctract coeficients from .37 file (file with NBOs) and put them into output file instead of mulliken polulation ceoficients or somethink like that …
      Jmol should also be capable of viewing NBOs but it requires .46 file which i could not obtain (with gaussian 03)

  37. Hola,
    Quisiera pedirle si es posible el programa Molekel 4.3.
    Muchísimas Gracias, siempre me es muy útil su blog

  38. Joaquin,
    Would you pleaseeeee!!!! send me molekel 4.3. If you have more than one OS even better. I have access to all three win OS, Mac OS (intel) and linux. I am more interested in the first one and the last one. Thanks a million for the help.

    • Hi Henry,
      If I remember correctly you have posted comments before, right? Perhaps since 2009 or early 2010.
      Anyhow, Molekel is now available, just go to the home page of this blog.

      Have a nice day

  39. Hola Dr. Joaquin Barroso:
    En primer lugar quisiera felicitarlo por su blog, realmete ha sido de gran ayuda.
    En segundo lugar tengo una consulta: quise realizar cálculos NRT para obtener las estructuras de resonancias y sus respectivos pesos de compuestos que no son TS. En una respuesta anterior encontre que solo eran para TS, sin embargo en la página de NBO mustra un ejemplo de una anális NTR para la formamida.
    El problema es que en el output no se genera el análisis NRT.
    Yo uso $nbo ntr $end, y el programa NBO 3.0.
    Debería utilizar otras keywords o es el programa. Si fuese lo segundo que alternativas tendrias para obtener la informacion de estructuras de resonacias (además del NBO 5.0).

    Desde ya muchas gracias.


    • Hola! Muchas gracias por tus palabras, que bueno que te ha servido la información contenida en este blog.
      Sobre el análisis NRT lamento decirte que sí es el programa. NRT no se encuentra disponible en NBO 3.x que es la versión incluida en Gaussian. No sé que otra alternativa exista a comprar NBO5.0. Intenta contactar a los creadores en su página. Yo te recomiendo comprar una licencia académica de NBO5.0 (como 100 USD para varios usuarios).

      Saludos y gracias por visitar!

  40. hi,
    Thanks for the blog. It’s priceless information that you have shared. I have a problem with the NBOView 1.0 version(linux). I have the output files from the gaussian 03 (NBO3.1 ) using the PLOT commoand of NBO. when i am trying to visualize the NBOs it is working fine except that It is not showing the bonds between the atoms in 3d renderning (view command in NBOView). I want to show the bonds . can you help me in this regard.

    thanks in advence

    Thirupathi. R

    • Hello Thirupathi,

      I’m sorry but I’m not familiar with NBOView. I’m sure there is a way to show those bonds, just play with the software. Try changing from one display format to another (wire, tube, ball&stick, etc.) this sometimes work in other programs.

      I hope this helps!

  41. Dear sir,

    I was using guassian 03 for running the program. I am calculating TD/DFT with 6-311++G(d,p) for my compound in gas phase I got the results. But I am doing the same calculation in sovent phase IEFPCM model, My input file is #p TD/DFT b3lyp/6-311++G(d,p) (IEFPCM= THF),
    I got the error message like this,
    “out of memory error, this program needs minimum memory to do this calculations”
    Please help me how to give input file for doing calculations in solvent phase.

    Thanks in advance,

    With regards,

    • Devi, you will need more memory for the calculation to go. You add the keyword %mem= 100MW. Or even a higher number if you have large computational resources. MW=megaword. If the message ipappears again, you will need to increase even more.

    • Hello Krishan,

      The error message is pretty self explanatory. Use the following in your input at the link0 section:


      repeat the calculation and if you get the same error, try increasing the value. Also check the ‘maxdisk’ keyword at the Gaussian website.

      I hope this helps!

  42. Aniruddha Ganguly

    Dear Dr. Barroso,
    Thank you for such a nice blog on NBOs. I am facing some problems in visualizing them in Molekel 4.3. To obtain the .47 file, at my computer, I have used the ARCHIVE option in the $NBO section as suggested by you and I got the file. I renamed it to a .orb file to load it in Molekel. However, When I’m trying to load it from Load> NBO orb option, there comes a message mentioning that it couldn’t be loaded. Would you please help me out?

  43. yesterday i was running one NBO calculation on a MP2 output with NLMO keyword to get the natural localized molecular orbitals and i got error termination with this error NBStor is confused about NOcc. I could figure out that this error is happening when i am using density=MP2 but when i remove this and the calculation is based on SCF density then i do not encounter any error.

    I a bit confused about this MP2 density and SCF density. In gaussian manual it says MP2
    Use the generalized density corresponding to the second-order energy. Can you please clarify as to when to use the MP2 density and when to use the SCF density


  44. Dear sir,
    How to write input file for calculating dimer of hydantoin-5-acetic acid in guassian 03.

  45. Dear sir,
    Greetings. How can i get density of states versus eV graph either by chemgraft or Gaussview 3 fron the output og Gasussian 03 NBO analysis.
    I have given in the route section pop= full and gfinput also.
    thank you sir
    thanks for the great helps you are offering for Gauss researchers.

  46. so, for the readers/users of this blog that want to use chemcraft, here is how to do it (at least for version 1.7, build 365).

    gaussian input:
    #P b3lyp/6-311++g** Opt pop=(full,nboread) gfoldprint geom=check guess=(read,only)


    0 1


    this will generate files from *.31 to *.41
    for the visualization of NBOs, you’ll need FILE.31 and FILE.37. open FILE.31 from chemcraft. it will automatically detect FILE.37 (if in the same directory).

    tools > orbitals > render molecular orbitals
    select the NBOs of interest (whcih are in the same order of the output), adjust the settings > OK.

    on the left side of the window, select the NBO of interest and then click on ‘show isosurface’. adjust the remaining settings. to represent another orbital, click on ‘keep this surface’ and then select another orbital from the rendered set and follow the previous steps.

    PS: if the gaussian job is run remotely, it is of uttermost importance to have space in the client where chemcraft is used. FILE.37 took a while to transfer/had a size of 0 bytes.

    it is possible to open a formated checkpoint file, containing the NBOs, in chemcraft.
    gaussian input:
    #P b3lyp/6-311++g** Opt pop=(full,nboread,savenbo) gfoldprint geom=check guess=(read,only)


    0 1


    the procedure is identical, but it is only necessary to read the *fchk file and then render the desired orbitals.
    however, two problems might arise:
    a) the orbitals in the chekcpoint are reordered, thus requiring some careful inspection of the output.
    b) sometimes, for a larger molecule, the checkpoint might not be properly saved and the gaussian job (as previously reported – ) will end with:

    Failed in SchOr1 in NBStor.
    Error termination via Lnk1e in /data/programs/g09/l607.exe at Wed Mar 6 15:27:33 2013.

    some self-promotion:

  47. Hi Dr. Joaquin,

    Thanks for your discussion. Its really very nice and helped me to understand the NBO analysis.
    Can you please post about the natural transition orbital analysis in Gaussian09?

    With best regards,

  48. Saludos estimado doctor,

    Muchas gracias por la ayuda que brinda a traves de su blog.
    Quiero realizar una consulta, estoy realizando un cálculo en G09 para visualizar los orbitales HOMO y LUMO con la siguientes keywords.

    #p B3LYP/6-311++g(d,p) td (singlets, nstates=15)

    El cálculo se desarrolla y finaliza con normalidad, pero al intentar abrir el file.chk, para visualizar los orbitales, con Gaussview 05, me muestra el siguiente error

    ERROR CONNECTION GFCHK::ReadFile() Cannot find file

    Que debo hacer, la verdad le estoy escribiendo un tanto desde la pura ignorancia, ya que soy novato en esto de los cálculos. Además, no se si estoy escribiendo en el lugar correcto de los post.

    Una cuestion más, que pienso no corresponde a este post, pero bueno. A manera general, como elijo el nivel de toría que resulte eficiente y correcto optimizar y realizar los cálculos en Gaussian para mi molécula, esto debido a que en una publicación reciente de un amigo, el refere envió una cuestion al respecto y quisiera saber si existe una manera fundamentada y metódica para realizar esto.

    De antemano, muchas gracias por la ayuda. Y disculpe tantas preguntas.


  49. Dear Joaquinbarroso,

    Thanks for a helpful site. I’m having problems identifying the weighting of the different types of bond character for my structure calculation. I am carrying out a trial calculation, based on work in the literature which says there are 3 different types of bonding (in the particular structure), some of which is ionic (44%) and the others are covalent (22 and 24%). When I repeat the calculation I do not get these weightings.

    Have you any idea about this?


  50. Dear Joaquinbarroso,

    Thanks for a helpful site, I learned lot from this site. I’m having problems identifying the weighting of the different types of bond character (TotalCovalent/ionic). I have seen in the NBO manual, under the Natural Bond Order: (TotalCovalent/ionic) it prints the type of character. I used the following key input for my calculation but in the output it doesn’t print the natural bond order. I am using G09/G03.

    # B3LYP/6-31G(d,p) Pop=NBORead

    Example of NBO bond orders

    0 1
    C 0.000000 0.665676 0.000000
    H 0.919278 1.237739 0.000000
    H -0.919239 1.237787 0.000000
    C 0.000000 -0.665676 0.000000
    H -0.919278 -1.237739 0.000000
    H 0.919239 -1.237787 0.000000

    $nbo bndidx $end

    Thanks in advance.

    Yours Sincerely

  51. Maryam Taimoory

    hi I am new in your blog. Could you please guid me with this problem. I have tryed to render the nbo orbital of my molecule which has 2 lone pair. But I do not know why in my output file I have onle one lone pair.

  52. Estimado Joaquin,
    Estoy recien formandome en quimica computacional y debo decirle que me parece genial su blog!
    mi interogante seria la siguiente:
    Segui el procedimiento descrito en el post para visualizar los Orbitales NBO y en efecto obtube una representacion de orbitales pero me intriga que estos orbitales no son locales sino que mas bien parecen OMs
    Es esto normal?? mi conocimiento sobre la teoria no es extenso quizas podria ser… pero de momento me parece incorrecto.

    • Es normal, ya que no son tan localizados como nos gustaría a los químicos. Te sugiero que hagas el mismo ejercicio con los orbitales canónicos (Orbitales Moleculares) y registres visualmente las diferencias.

      Muchas gracias por tus lindas palabras sobre este blog, me da gusto saber que te ha sido de utilidad.


  53. Hello ,
    I have a question, I did simple calculation
    #P B3LYP/6-311++G(3df,2pd)


    0 1
    23 1.59 ….

    I got output file with normal termination. I tried to open this with gaussview03 but it gave me error operning chk file ! ( i want to see homo LUMO) I read your comment for Ivonnet on 2010 that there has to be some fixing in output file like Atom AN; etc. Do you have any idea what should I do with this out put file which can be open by gaussview03.

    • Hi Rosha

      I think the easiest would be to just change your visualizing software by either updating GaussView or by downloading something different like Chimera.
      Try that fixing from the comment but if it doesn’t work then change software.

      Have a nice day!

  54. Hi Dr,
    I’m having a problem running genecp/qzvp with nboread/bndidx command, the output file giving me error


    Here is my input file, any idea what i did wrong?
    Thank You

    %chk=C:\Users\Nazmi\Desktop\Nov13\Hybrid\Be\Acn Be NBO BNDIDX Hybrid.chk
    # opt freq rb3lyp/genecp geom=connectivity pop=nboread

    Title Card Required

    2 1
    C -1.99929000 -0.44546000 -0.00013500
    H -1.78957100 -1.51305800 0.00022800
    H -3.04308900 -0.13447000 0.00055200
    C -1.01685600 0.51008800 -0.00004700
    H -1.23374400 1.58299100 0.00014600
    C 0.32300400 0.18133300 -0.00001600
    N 1.48782800 -0.04095600 0.00003600
    Be 2.95261400 -0.28113300 0.00000200

    1 2 1.0 3 1.0 4 2.0
    4 5 1.0 6 2.0
    6 7 3.0
    7 8 1.0

    H C N 0
    Be 0

    Be 0


    • Hello there!

      I think you should include the pseudo=read keyword in your route section and you should be fine.

      Have a nice day!

      • Hi again,
        Thank you Dr, the job can run perfectly now, really appreciate it.
        Can u advice, what’s the differences when u ran a job with/without the pseudo=read keyword

      • Well, you had the basis set lines correctly (and they were read by the gen keyword) but after the basis (which ends with the line ****) you had a pseudopotential (or effective core potential) explicitly defined for a given atom but since you never told the program in the route section that a pseudopotential was to be used (pseudo=read) then the program didn’t know what those lines were. See what I mean?

        Glad I could help!

  55. Sir, I hope you are fine and also I pray for this. I have some trouble. I was did NBO calculation for a molecule having triple bond. I assigned BD 1 as sigma and BD 2 as bi symbol respectively. But I don’t know how to represent triple bond symbolically. I need your instructions.

    • Dr Mr. Premkumart,
      The designation of bonds as single, double, or triple is not necessary for any ab initio calculation. You will get the same NBO’s for a triple bond (one sigma, and two perpendicular pi bonds) whether or not there are three lines between the carbons as drawn in your build software.
      For example, as the Guest user on the Demo account at the WebMO webpage (see jobs 150133-150136) I just built propynal first with double and triple bonds drawn in explicity, optimized with B3LYP/6-31G*, and did an NBO job. You can see the NBOs by going to the bottom of the Results page. Then I started with the optimized geometry, changed the multiple bonds to single bonds (by right-clicking the bond and checking “single”), and did the same two calculations. These are named “…norep” . The geometry and NBOs are exactly the same.
      You can log on to this website as Guest, as I did, and look at these jobs and output.
      The URL for WebMO is
      Best Regards,
      John Keller
      University of Alaska Fairbanks

  56. Estimado Doctor:

    Estoy intentado realizar la visualización de datos con GaussView 5.0 y los archivos *.fchk y *.fch son generados y visualizados sin problema a partir de *.chk, sin embargo en Edit –> MOs la pestaña de “Visualize” no me aparece activa por lo que me es imposible visualizar los orbitales.

    ¿Sabría a qué es debido?

    Espero su respuesta

    Muchas gracias

    • Hola Pilar,

      Posiblemente se deba a una incompatibilidad de la arquitectura de los procesadores en los que calculaste contra los que usas para visualizar (32 y 64 bits). Sin embargo, si todo lo calculas y visualizas en la misma computadora puede tratarse de un problema del mismo GaussView.
      Mi recomendación es que al obtener el chk uses formchk -3 file.chk file.fchk
      la opción -3 genera un archivo fchk más grande con más información (nuevamente, si estás cruzando entre procesadores con diferente arquitectura esto no va a funcionar). La otra es que uses la variable SAVENBOS en el route section como pop=(full,NBORead,SaveNBOS), por ejemplo, y luego uses la utilidad cubegen para generar cada uno de los orbitales de tu interés. Es un poco más laborioso pero te dejas de problemas.

      Espero que te sirva pero si acaso no es así estoy disponible para lo que se te ofrezca.


  57. Excellent poste : je pense en discuter dans la journée avec mes collègues

  58. Sergio Dasilva

    Hola, tengo una inquietud, yo he tratado de generar un ploteo con Gaussview 05 usando orbitales moleculares con EPS y siempre me sale neutro los graficos. en Gaussview 03 se generan bien mostrando los distintos puntos isoelectricos. sabes si hay que agregarle un comando adicional para generarlos?

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  60. Une fois de plus un très bon article : j’espère en discuter dans la
    journée avec mes collègues

  61. This website was… how do I say it? Relevant!!
    Finally I’ve found something which helped me. Thanks a lot!

  62. Hi Dr
    I can not create cube files from. fchk
    eror: The Cub Man. Utility Failed

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  68. Hello.
    I am using the gauss view but i can’t change the phase of the orbitals. Also, i am using the following keyword:

    %chk=name of file.chk
    # b3lyp/aug-cc-pvdz pop=nbo6read

    Title Card Required


    $nbo aonbo=c $end

    Can you help me?

    • Hi!
      What do you mean you cant change the orbitlas phase? Please give me more information so i can helo you better.
      Im not familiar with nbo6read didn’t you mean nboread?
      Ill help you as soon as you let me know some more about this issue.

      Best regards

      • I understood his question.
        When you plot NBO orbitals, sometimes the phase is not that one would expect. It gives inverse phase when it would be a bonding interaction. Prof. Weinhold explained that there is any problem with phases in NBO website FAQ (question 21):
        That is possible to change the orbital version in NBOView by using a SIGN keyword. I don’t know how to do it in Gaussview either. Any ideas?

  69. Hi, thanks for that information about NBOs, but now I not need it. Can you help me in my question which is that how can I define ortho and para hydrogen isomers in gaussian 03?

  70. Dear Sir,

    Can IR calculation of my compound in different solvents done using Gaussian ?

  71. Dear Sir,

    I have Gaussian 09 Rev.D01 and NBO 6.0. How to draw the 3d orbitals (xy, xz, yz, x2-y2 and 3z2-r2) such as Co atom in terms of AO and NAO basis, separately; in GaussView or any visualization programs. Thank you so much.
    Have a nice day.

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  73. Hello Dear

    I computed NBO using firefly/PC-Gamess 8.2.0 in which NBO program 5.9 is implemented. My question is that how I plot NBO from firfly output file using Jmol , JmolNBO etc

    • I’m not sure it can be done. Maybe if you use the SaveNBOS option during the calculation and then open the chk or the fchk file in any of those you can get it done. Try doing it also with some cannonical orbitals just to make sure you are getting a different set.

      i hope this hels

    • I’m afraid I haven’t used any of those programs before so I cannot advice you on how to do it. Please, if you figure out how to, share it with us; we’d be thrilled to do a guest post about it!

      Have a nice day

  74. Dear Dr. J. Barroso, How about the notation of NBOs? I mean, if frontier MO are noted as HOMO and LUMO; can we denominate the frontier NBOs as HO-NBO (highest occupied NBO) and LU-NBO (lowest unoccupied NBO)? Correspondingly, HO-NBO(-1), HO-NBO(-2), LU-NBO(+1), LU-NBO(+2), etc.

    The second question is related to the comparison between MO and NBO for the same molecule.
    For example, if MO#114 is HOMO (delocalizated) and NBO#114 is HO-NBO (localizated): are these orbitals (HOMO and HO-NBO) equivalent in terms of “”2e source”? i mean we will have the same 2e, but for HO-NBO they are localizated whereas for HOMO the same 2e are delocalizated; is this interpretation correct?
    Thank you for your time and consideration,
    with best regards, Corneliu

    • Dear Corneliu,

      Indeed we could label NBOs the way you say in your first paragraph; I haven’t seen that ever and maybe there is a reason but I don’t see any reason against that labeling system.
      Regarding the equivalence of MOs and NBOs the answer is no. NBOs come from the re-orthonormalization done on the basis of the chosen basis set, hence MOs and NBOs are constructed diferently and should not be compared. However, they should give rise to the same electron density.

      I hope this helps

  75. Dear Dr. Barroso,

    thanks a lot for your amazing blog. Regarding visualizations of NBOs with Gaussview and Chemcraft, I have a question. In general, after generating the .47 file and using GenNBO to create the plot files, chemcraft works very well to visualize NBOs. In some cases however, after generating all plot files (31-42), Chemcraft is not working with error like: list index out of bounce. Also Gaussview will not work in these cases (using savenbo). Nevertheless, optimization and frequency calculation are well converge and all jobs terminated normally. Are you familiar with such problems?
    Thanks again a lot.

    • Hi Niklas,
      Thank you for your kind words about my blog, I’m glad you’ve found it useful.
      I haven’t worked with Chemcraft in a while but maybe if you try using the checkpoint or the formatted checkpoint it could work (provided you used the savenbos option, of course). You also mentioned the generation of files 31-42, is this a typo? Didn’t you mean 31-47? you need your 47 file.

      I hope this helps

      • HI,
        thanks a lot for the quick reply. In 99% of my calculations visualizing NBOs with Chemcraft works just fine. In the case described above I generate the 31-47 files and they seem ok, as well as the NBO6 output file. Somehow Chemcraft can’t open the files though with an error message like: Excpetion Estring error in module chemcraft.exe at 00000000000. List index out of bounce(2).
        As I specified savenbo, I tried to visualize the NBOs with Gaussview 5, but gaussview can’t open the chk or fchk files, due to an error that you already discussed before (indepenent vs independant, number of basis functions vs number of independant basis functions). So I think somehow it is related to that. What would be a way to deal with this problem? fix the .fchk file, then generate a new .chk file to use as input for pop=NBOread,savenbo ($NBO archive $END)?
        Thanks again for your help.


      • Hi Niklas, I already tried both options and they both work. I’m sorry but I don’t know what could be the problem, I suggest you find a chemcraft forum, perhaps.

  76. Satyajay Mandal

    Bogus,er cheye to puro periodic table dite paris bhai

  77. Francisco Núñez Zarur

    Buenas tardes profesor Joaquin. De antamano felicidades por tu blog, me ha sido de gran ayuda. Tengo una duda respecto a NBO: quiero visualizar algunos NBOs usando pop=nbo6read y usando las keyword PLOT. Resulta que si uso una base all-electron me genera los archivos de visualización sin problemas, sin embargo, cuando uso un ECP (para un metal) no me lee la linea $NBO …. $END. Sabes si hay alguna forma de evitar esto?

    PD: no estoy obligado a usar un ECP pero sería más cómodo por tiempo.


    Francisco Núñez Zarur

  78. When I am give plot option down to .com file, l607 error is coming. After deleting the plot option, the job is running. But i am not able to view nao or nlmo orbitals. How to rectify this problem



    Dear Dr. Joaquin Barroso,
    This is very nice and useful blog for theoretical chemistry learner like me. I could not get Molekel 4.3. please provide the Molekel 4.3 software.
    please help me.
    Thank you very much

  80. Hola Dr. Barroso. Quería hacerle una consulta sobre el uso de los NBO. Permitiría diferenciar cuáles confórmeros de una molécula son los más estables y porqué?

    Saludos y gracias!

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