ADL: Autodock Vina

Oleg Trott trott at
Tue Jun 16 02:14:47 PDT 2009


On Tue, Jun 16, 2009 at 12:12 AM, hazizian<hazizian at> wrote:
> I used Autodock vina, I have 3 problems:
> 1- at the first job it wasn't successful, since the ligand jumped out of the
> grid box (grid box is big enough to include the whole protein.)
> (all the binding energys are zero), it seems there is no atempt to enter the
> ligand to grid box .

I've never seen this happen. Please submit a bug report as described here:

Note that your bug report should include all of these (9/10 left):

* the exact error message (if any) or description of the problem,
* your version of the program,
* the platform you are running it on,
* all command line options,
* configuration file (if used)
* ligand file as PDBQT
* receptor file as PDBQT
* flexible side chains file as PDBQT (if used)
* output file as PDBQT (if any)
* random seed the program used (this is printed when the program starts).

If any of these are missing, the problem can not be investigated.

(It seems that some people are having trouble understanding the
concept of exact reproducibility and its necessity. How can I explain
it better? Suggestions are welcome)

> 2- I want to define spacing 1.000 insted of 0.375, but there is not any arg
> for specifiying this option.
> 3- when I want to try another job this messege appeares:
> out of memory error, what is this memory is it apart from current memory of
> computer?

In this case, "out of" means "not enough", i.e. you don't have enough
available RAM for the program's needs, given the task you've assigned
to it


Oleg Trott, Ph.D. (Columbia University)

More information about the autodock mailing list