Using a VMD script written by me (MOisoall.tcl) I try to visualize the behavior of HOMO in the course of an inversion of ammonia (Fig. 1), but the VMD script does not work correctly (Fig. 2). Could someone check the MOisoall.tcl script and correct it ?. I attach the .cub files of the three-point HOMO of said reaction (MO_SP000 * .cub).
NOTE: to run the script it is necessary to move the .cub and MOisoall.tcl files to the VMD directory and write:
source MOisoall.tcl
in the VMD console (Fig. 3) and press the Enter button.
Hey,
It's almost true :)
Everytime you load a molecule, vmd gets a unique molecule number. So we usually use "top" statement to avoid explicitly define and work with that molecule number.
In other words, you just need to learn the molecule number and call this number where it is needed. Just check the edited script in attachment and I think it will work :)
Cheers,
Ali
It is correct, thank you very much.
Could you answer another question that I posted earlier:
https://www.researchgate.net/post/How_to_control_the_UNION_THRESHOLD_in_VMD?_ec=topicPostOverviewAuthoredQuestions&_sg=xrCIWCjdCgVH1sjjqRXCOc3hLdKq1AQkhE-P7mjiiuAih5_lUPtyE7Bg1CiMB7K7WSKT6FhK47mfe28I
- Badges
- Science topic
- Similar topics
- Linguistics
- Composition Studies
- Writing