ADL: regarding active site
trott at scripps.edu
Wed Jun 17 19:53:29 PDT 2009
On Wed, Jun 17, 2009 at 7:12 PM, Davide
Mercadante<dmer018 at aucklanduni.ac.nz> wrote:
> Hi Oleg,!
> I tried the running of Vina as you showed on the tutorial and you were
> alright, I solved the problem. Vina doesn't allow the ligand to jump the
> site where I placed the grid. The calculations are really fast compared to
> Autodock and I advice everyone from my own experimence to use Vina.
> However, I have two questions:
> the flag "all" in the parameter file doesn't seem to be recognized and Vina
> (on an ubuntu machine) gives you an error. Without the flag is all fine. In
> this case the output is written to an output file that starts with the name
> of the ligand pdbqt file.
This is explained on top of the tutorial page, above the video.
> I have visualized this output (using a text editor) and it shows all the
> conformations in the pdbqt file.
I take it that you are trying to say that there is more than one model
in the PDBQT?
> I have opened the file using pymol but the
> software is able to visualize only the first conformation I think and
> doesn't show all the conformers:
> 1) I need to modify the pdqt file and save it in some other format to
> visualize all the conformers? If yes, how?
The version I have has no problems there. Try "->" key. Failing that,
post a screenshot and your output file.
> 2) there is an option to cluster the conformations as in autodock and to
> have the graphs of rmsd Vs the number of conformations fo r an rmsd given
Vina does "clustering", i.e. avoiding redundancies automatically
without asking. Please read the paper if you need to know more.
Best of luck,
Oleg Trott, Ph.D. (Columbia University)
More information about the autodock