|
It is currently Sat Apr 21, 2018 12:07 am
|
View unanswered posts | View active topics
 |
|
 |
|
Author |
Message |
arcady
|
Post subject: protein model is not cleaning up properly Posted: Tue Mar 16, 2010 10:19 pm |
Joined: Tue Mar 16, 2010 10:07 pm Posts: 2
|
here is what I get (the pdb file is sendaimt.pdb in ARCFOLDER)
Traceback (most recent call last): File "tools/prepare_receptor4.py", line 168, in ? delete_single_nonstd_residues=delete_single_nonstd_residues) File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 520, in __init__ version=version, delete_single_nonstd_residues=delete_single_nonstd_residues) File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 120, in __init__ self.repairMol(mol, self.repair_type_list) File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 161, in repairMol self.newHs = self.addHydrogens(mol) File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 174, in addHydrogens HB.addHydrogens(mol) File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/MolKit/hydrogenBuilder.py", line 81, in addHydrogens hat = AddHydrogens().addHydrogens(mol.allAtoms, method=self.method) File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/PyBabel/addh.py", line 92, in addHydrogens Hatoms = self.place_hydrogens1(atoms, num_H_to_add) File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/PyBabel/addh.py", line 156, in place_hydrogens1 Hat = Hat + self.add_vinyl_hydrogens(a ,SP2_C_H_DIST) File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/PyBabel/addh.py", line 444, in add_vinyl_hydrogens c3 = c2.bonds[1].atom1 File "/usr/lib/python2.4/UserList.py", line 28, in __getitem__ def __getitem__(self, i): return self.data[i] IndexError: list index out of range
-- any suggestions?
Thank you!
Arcady
|
|
|
|
 |
hazaie
|
Post subject: Re: protein model is not cleaning up properly Posted: Wed Mar 17, 2010 12:20 pm |
Joined: Wed Oct 29, 2008 2:24 pm Posts: 40
|
Probably there was a probleim with your protein. Could you please upload your protein and leave it there, so I can further check the problem?
Thanks Eszter
|
|
|
|
 |
arcady
|
Post subject: Re: protein model is not cleaning up properly Posted: Wed Mar 17, 2010 4:51 pm |
Joined: Tue Mar 16, 2010 10:07 pm Posts: 2
|
Eszter,
I think I did yesterday, and I uploaded it (I think) again, with the same error message. Is there a way to send you a pdb file if you do not see it?
Thank you!
Arcady
|
|
|
|
 |
hazaie
|
Post subject: Re: protein model is not cleaning up properly Posted: Thu Mar 18, 2010 12:59 pm |
Joined: Wed Oct 29, 2008 2:24 pm Posts: 40
|
Dear Arcrady, Please send your pdb file to the following emailaddress: info@dockingserver.com, so I can analyze the problem. Thanks Eszter
|
|
|
|
 |
hazaie
|
Post subject: Re: protein model is not cleaning up properly Posted: Fri Mar 19, 2010 10:04 am |
Joined: Wed Oct 29, 2008 2:24 pm Posts: 40
|
Dear Arcady,
we have upgraded the DockingServer to handle your protein, it should work now.
Kind Regards, Eszter
|
|
|
|
 |
|
|
 |
|
 |
|
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
|
|