I have problem to create sigma and pi hole surfaces and create the extrema of esp. what are the relavent softwares that may help?
Multiwfn (http://sobereva.com/multiwfn) should be the best choice, it is free, flexible and quite easy-to-use. Its main function 12 can directly give you ESP minima and maxima on vdW surface. Please check Section 4.12.1 of Multiwfn manual for example. If you want to plot more pretty graph, you can use it in combination with VMD program, please check Section 4.A.13 of the manual for detail.
Thanks Riaz A. Khan , I will have it in mind whenever I can have the licence for hyperchem, right now, that is unavailable to me..
Tian Lu , many many thanks for your answer, I have been using Multiwfn for sometime. I have some questions regarding the execution of the software....
1. How many surface extremas can the software show as an output?
2. If I load a fine quality ESP cube file, it crashes sometime.
3. Can we change the colors of the maximum and minimum lebels? vide: clipboard01.jpg, right side image.
4. This might be an out of the topic question still,
I have been using another software where in the route section i had to add "nosymm 6d 10f" keyword extra along with usual optimization keywords+basis sets etc. Let this be old.fch.
the problem was that, when I used the old.fch and calculate the surface extremas by multiwfn it shows ~10000 Kcal/mol. whereas the same molecule without those keywords show ~22Kcal/mol. What could be the possible reason?
Thank You in advance,
1 This mainly depends on the actual character of your system. There is no upper limit in the Multiwfn
2 The reason is unclear, it is better to send me the compressed ESP cube file and show me all of your operation steps so that I can figure out the reason.
3 You cannot change the color in Multiwfn, but you can easily change the color in VMD.
4 I am not sure, it is also better to send me the old.fch file as well as the corresponding .gjf file so that I can have a check. In principle, these keywords should not result in such a strange phenomenon.
Hi:
I have some questions about Multiwfn .
1. I loaded a Gaussian cub of electronic density of a molecule with about 45 atoms.
2. The ESP maxima and minima values calculated with Multiwfn show only positive values. The molecule is its neutral state and contains O and N atoms, therefore we should expect some negative values for ESP. (¡?¡?)
3. Multiwfn looked specially interesting to me because of the possibility of including the ESP maxima and minima in the surface. But all the extra work with photoshop is too much. Do you intend to modifiy this section?
Regards,
Juan
Juan-Sebastián Gómez-Jeria
Hello,
1,2 You should not use cube file as input file, because cube file doesn't record any wavefunction information. You should use one of supported formats that carries wavefunction information, such as .fch, .molden, .wfn, .wfx ..., please check Section 2.3 of Multiwfn manual on how to properly choose input file, and check Section 4.12 for analysis examples.
3 In the post-process menu of main function 12 there are several options:
"3 Discard surface minima in certain value range"
"4 Discard surface maxima in certain value range"
"18 Discard some surface extrema by inputting their indices" (this option is only available in very recent versions)
Clearly, you can use these options to remove unwanted surface extrema according to value of mapped function or index range. In addition, if you intend to use VMD to plot the extrema generated by Multiwfn, in the "graphics" - "Representation" panel, you can manually input indices of surface extrema (e.g. serial 1 5 to 20 19) in "Selected atoms" box to make VMD only show the extrema of interest.
Best,
Tian
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