silvergirl wrote: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.
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.
dielectric -0.1465 # <0, AD4 distance-dep.diel;>0, constant
jmeans wrote: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>
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
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