I want to ask you what is difference between Autodock Tools and Autodock Vina, where is difference what we can do with Autodock Tools that cannot do with Autodock Vina and conversely
As far as I know, Autodock Vina is the next iteration of the software. The input looks little bit different, for example the search grid input is in angstroms not pts. Vina also uses (they say) more precise algorithm.
For me the main difference is that Vina can run in multiple threads, so you can parallelise it, and it's faster so it's more suitable for let's say screening compared to docking of few ligands.
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version 2.3.6
how to show (play) conformations of docking with autodock Vina
You want to see the visualization? Vina output is a pdbqt file, which is just like a regular PDB (with the addition of atom charge property), so the PyMol or whatever you use can display it. You can also strip the column, I think it's 11th, to make it a regular PDB. AutoDock has a very good FAQ and help pages, you should start looking there in the first place.
In Pymol I can to see but I want to do Analyze of conformations example from1-9as in Autodock Tools and to save each as pdb and then to see each conformation binding to target examole with discovery studio
I may to see each conformation in pymol but how to save session as pdb then to open it with discover studio to analyze interaction ligand-protein. how to save from pymol as pdb .
and how to show analyze of work with vina in ADT
Not sure what you mean by "how to save from pymol as pdb", PyMOL already reads PDB. I think you should read up a little bit on the documentation, it's not that difficult to get the fundamentals and than ask more specific questions here.
How to use ADT to analyze vina results, I have open ADT and "open dock vina result" but when I try to show conformation or cluster don`t execute because say that "no molecules with dockings in viewer"
I have result from vina but I want to show conformation and cluster in adt and to save each conformation in pymol and to save it then to show interaction
I have result from vina whereI have 9 conformation but now I have open with pymol and I have seen ligand-receptor (each) but I want to save as pdb each and to open then with discover studio or chimera to show type of interaction
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how to fix this problem and to show successfully my result of vina docking in ADT
or what other software can I use for analyzing my docking that I perform with vina
I reiterate - there is a reason people are not responding to you. Look back at what others have asked of you and you'll know why. And I hope you're running the program the right way because python code execution shouldn't open up IDLE, ideally. Again, switch to Linux.
yes yes, but I have never use with ubuntu and I installed it but it's so difficult to work with it
what are other options to show analyzing of vina results
Get a bioinformatics person near you to help you out. You are being not entirely helpful in giving proper diagnostic information to people online and you are also unable to follow our instructions. You will definitely benefit from having a bioinformatics or even an IT person take a close look at your problem physically.