The Molecular Graphics Laboratory Forum

AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
It is currently Sat Jul 21, 2018 10:48 pm

All times are UTC

Post new topic Reply to topic  [ 1 post ] 
Author Message
PostPosted: Fri Jul 04, 2014 3:37 pm 
Millimolar User
Millimolar User
User avatar

Joined: Fri Jul 04, 2014 3:26 pm
Posts: 1
Hello !

We have prepared a protein with an other software (that add the charges as we want) and we would like to keep theses charges so we tried with -C option which is supposed to preserve all input charges. However prepare_receptor4 did not convert our molecule in pdbqt and display this error : -v -r protein.mol2 -A none -C
set verbose to True
set receptor_filename to protein.mol2
set repairs to none
do not add charges
read protein.mol2
setting up RPO with mode= automatic and outputfilename= None
charges_to_add= None
delete_single_nonstd_residues= None
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/AutoDockTools/Utilities24/", line 179, in <module>
File "/usr/lib/python2.7/dist-packages/AutoDockTools/", line 546, in __init__
version=version, delete_single_nonstd_residues=delete_single_nonstd_residues)
File "/usr/lib/python2.7/dist-packages/AutoDockTools/", line 140, in __init__
self.addCharges(mol, charges_to_add)
File "/usr/lib/python2.7/dist-packages/AutoDockTools/", line 212, in addCharges
File "/usr/lib/python2.7/dist-packages/AutoDockTools/", line 211, in <lambda>
len_zero_charges = len(filter(lambda x: x.charge==0,
File "/usr/lib/python2.7/dist-packages/MolKit/", line 407, in __getattr__
return self._charges[self.chargeSet]
KeyError: None

Do you have any idea of what can trigger this problem ?

Thanks a lot for your help !

Display posts from previous:  Sort by  
Post new topic Reply to topic  [ 1 post ] 

All times are UTC

Who is online

Users browsing this forum: No registered users and 2 guests

You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Search for:
Jump to:  
Translated by MaĆ«l Soucaze © 2009