Frodo: Created page with ""no viable poses" error is a catch all error. This error just means that no viable poses were generated, it could be that the grids might be too small, although there might..."

2017-11-25T18:05:59Z

Created page with ""no viable poses" error is a catch all error. This error just means that no viable poses were generated, it could be that the grids might be too small, although there might..."

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"no viable poses" error is a catch all error.

This error just means that no viable poses were generated, it could be that the grids might be too small, although there might be some other reason.

To make the grids bigger I suggest using the following blastermaster parameter:
--box_margin=BOXMARGIN
specify the margin to perform grid generation
(important or covalent docking) (default: 10.0)

This parameter will define the space between the matching spheres and the edge of the vdw box.
Note that the effective box size is written out in the OUTDOCK file, DOCK will use the intersections of all the grid boxes.

There are other things to try to increase sampling:

For production run discovery screens, I would use the bold values,
but, to enhanced sampling, I recommend modifying the parameters below as follows:

* matchgoal 1000 -> 5000 ( 1000 for production docking, increasing this number will allow more orients and so will increase sampling)

* miminize yes (We have added in a minimizer since Ryan's paper. This parameter turns on the simplex mimization)

* bump_maximum 20.0 # stop examining any part of the molecule in which the van der Waals score in kcal/mol exceeds the parameter value
* bump_rigid 20.0 #discard the rigid component of the ligand molecule if the van der Waals score in kcal/mol for is above the parameter

By increasing these two bump parameters you will give the minimizer the opportunity to save more poses. e.g. increase both to 500.

* number_save 1
* number_write 1 (by increasing these two parameters to say 10 more poses will be minimized and written to the mol2 file).

Here is more information on the INDOCK file:
http://wiki.docking.org/index.php/INDOCK_3.7

Here is more information on the minimizer:
http://wiki.docking.org/index.php/DOCK3.7_INDOCK_Minimization_Parameter

No viable poses - Revision history

Frodo: Created page with ""no viable poses" error is a catch all error. This error just means that no viable poses were generated, it could be that the grids might be too small, although there might..."