Docking multiple ligands in PyRx

[silvergirl]

Is there any way of choosing ~1000 small molecules for docking in PyRx without having to pick them one by one? Thank you.

[sargis]

You can use Shift-Click to select multiple ligands at once: http://www.ehow.com/how_4716735_select- ... click.html
We had a user who run virtual screening with ~30,000 ligands. It takes long time though to run large number of jobs remotely. I recommend starting with ~10 ligands to get a feeling on how long it would take.

Thank you for using PyRx!
Sargis

[silvergirl]

When I press the "Add ligand" button on the "Select molecules" tab, the new window that appears only allows me to select and open one ligand at a time (shift button does not work).

[sargis]

Thanks. I've added an option for opening multiple molecules at http://sourceforge.net/apps/trac/pyrx/changeset/94

This will be available in the next release. In the meantime, please use Open Bable widget that can read a single sdf containing multiple molecules and convert then to ligand pdbqt all at once.

[silvergirl]

That has just solved my problem. Thank you.

[silvergirl]

I am trying to use autodock vina on PyRx to dock ligands with proteins which exist in some special solvents. those solvents have different dielectric constants and they are very different from water. Can the dielectric parameter used by autodock vina be set to other value? If not, can I do it using autodock on PyRx? Thank you.

[sargis]

I am trying to use autodock vina on PyRx to dock ligands with proteins which exist in some special solvents. those solvents have different dielectric constants and they are very different from water. Can the dielectric parameter used by autodock vina be set to other value? If not, can I do it using autodock on PyRx? Thank you.

I did a quick search and found this topic about Dielectric permittivity in Autodock Vina - viewtopic.php?f=12&t=1367

Regarding, AD 4, I found the following in AutoDock 4.2 User Guide: http://autodock.scripps.edu/faqs-help/m ... rGuide.pdf

dielectric <float>
[-0.1465]
Dielectric function flag: if negative, AutoGrid will use distance-dependent dielectric of Mehler and
Solmajer; if the float is positive, AutoGrid will use this value as the dielectric constant. AutoDock4
has been calibrated to use a value of –0.1465.

I just checked one of the gpf generated by PyRx and it includes the following line there:

Code: Select all

dielectric -0.1465                   # <0, AD4 distance-dep.diel;>0, constant

It's possible to change this and rerun AutoGrid through a command line without using PyRx, but I wouldn't do that since, as it's mentioned in AutoDock 4.2 User Guide, AutoDock4 has been calibrated using this value.

[jmeans]

I recently installed the current version for Mac (0.8), and it is working fine. I tried to replace the appropriate .py files with the three that were posted for selecting multiple molecules, since I need that feature, but PyRx would throw an error just after loading the content in the top half of the program window. Through some troubleshooting steps, I found that the wxMainFrame.py script is the culprit. When I restore the original .py file, PyRx starts up with no problems. The text of the error is below:

Traceback (most recent call last):
File "/Library/MGLTools/PyRx/runPyRx.py", line 71, in <module>
startPyRx()
File "/Library/MGLTools/PyRx/runPyRx.py", line 39, in startPyRx
frame = MainFrame(None, -1, size=(width, height-200))
File "/Library/MGLTools/PyRx/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/wxMainFrame.py", line 161, in __init__
from vtkAdaptor import vtkAdaptor
ImportError: No module named vtkAdaptor

[sargis]

I recently installed the current version for Mac (0.8), and it is working fine. I tried to replace the appropriate .py files with the three that were posted for selecting multiple molecules, since I need that feature, but PyRx would throw an error just after loading the content in the top half of the program window. Through some troubleshooting steps, I found that the wxMainFrame.py script is the culprit. When I restore the original .py file, PyRx starts up with no problems. The text of the error is below:

Traceback (most recent call last):
File "/Library/MGLTools/PyRx/runPyRx.py", line 71, in <module>
startPyRx()
File "/Library/MGLTools/PyRx/runPyRx.py", line 39, in startPyRx
frame = MainFrame(None, -1, size=(width, height-200))
File "/Library/MGLTools/PyRx/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/wxMainFrame.py", line 161, in __init__
from vtkAdaptor import vtkAdaptor
ImportError: No module named vtkAdaptor

Thank you for the message. The vtkAdaptor module is something new added in 0.9 version. I have been looking for a support to make this new release for Mac and Windows, but no luck so far - https://sourceforge.net/donate/index.ph ... _id=280633

My advice is to install 32-bit Linux virtual machine to check the new features from 0.9 version.

Thank you for using PyRx!