The Molecular Graphics Laboratory Forum

AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
It is currently Mon Jan 22, 2018 4:15 am

All times are UTC




Post new topic Reply to topic  [ 2 posts ] 
Author Message
 Post subject: pdbqt CH3CN
PostPosted: Wed Jan 22, 2014 10:12 am 
Offline
Millimolar User
Millimolar User
User avatar

Joined: Wed Jan 22, 2014 9:39 am
Posts: 2
Hi all,
When I use adt to process CH3CN to produce pdbqt files ,it always gives the following error.


"Traceback (most recent call last):
File "/home/yanyuna/Programs/autodock_adt/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/ViewerFramework/VF.py", line 898, in tryto
result = command( *args, **kw )
File "/home/yanyuna/Programs/autodock_adt/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/autotorsCommands.py", line 1008, in doit
initLPO4(mol, cleanup=cleanup)
File "/home/yanyuna/Programs/autodock_adt/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/autotorsCommands.py", line 292, in initLPO4
root=root, outputfilename=outputfilename, cleanup=cleanup)
File "/home/yanyuna/Programs/autodock_adt/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 1019, in __init__
detect_bonds_between_cycles=detect_bonds_between_cycles)
File "/home/yanyuna/Programs/autodock_adt/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 768, in __init__
delete_single_nonstd_residues=False)
File "/home/yanyuna/Programs/autodock_adt/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 143, in __init__
self.addCharges(mol, charges_to_add)
File "/home/yanyuna/Programs/autodock_adt/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 229, in addCharges
chargeCalculator.addCharges(mol.allAtoms)
File "/home/yanyuna/Programs/autodock_adt/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/MolKit/chargeCalculator.py", line 80, in addCharges
babel.assignHybridization(atoms)
File "/home/yanyuna/Programs/autodock_adt/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/PyBabel/atomTypes.py", line 127, in assignHybridization
a.babel_atomic_number = self.get_atomic_number(a.babel_type)
File "/home/yanyuna/Programs/autodock_adt/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/PyBabel/atomTypes.py", line 95, in get_atomic_number
_name = string.upper(name[0])
IndexError: string index out of range"


Who can help me with it ? Thank you vmey much


Top
 Profile  
 
 Post subject: Re: pdbqt CH3CN
PostPosted: Tue Feb 04, 2014 11:37 pm 
Offline
Picomolar User
Picomolar User
User avatar

Joined: Sun Jun 21, 2009 11:37 pm
Posts: 163
You could use obabel for this (it is included in the latest version of MGLToolsPckgs):
1. First create a file "ccn.smi" which contains the string CCN
2. Then use obabel to convert the contents of ccn.smi to pdb
(modify the path to locate your local copy of obabel) :
../bin/obabel -ismi ccn.smi -opdb -p7.0 --gen3D
3. Here is the resulting output:
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.2
HETATM 1 C LIG 1 1.018 -0.090 -0.049 1.00 0.00 C
HETATM 2 C LIG 1 2.537 -0.103 -0.051 1.00 0.00 C
HETATM 3 N LIG 1 3.031 -1.473 -0.063 1.00 0.00 N
HETATM 4 H LIG 1 0.650 0.941 -0.048 1.00 0.00 H
HETATM 5 H LIG 1 0.619 -0.592 0.839 1.00 0.00 H
HETATM 6 H LIG 1 0.617 -0.591 -0.936 1.00 0.00 H
HETATM 7 H LIG 1 2.915 0.418 0.834 1.00 0.00 H
HETATM 8 H LIG 1 2.910 0.425 -0.935 1.00 0.00 H
HETATM 9 H LIG 1 2.714 -1.960 0.774 1.00 0.00 H
HETATM 10 H LIG 1 4.049 -1.467 -0.022 1.00 0.00 H
CONECT 1 2 4 5 6
CONECT 1
CONECT 2 1 3 7 8
CONECT 2
CONECT 3 2 9 10
CONECT 4 1
CONECT 5 1
CONECT 6 1
CONECT 7 2
CONECT 8 2
CONECT 9 3
CONECT 10 3
MASTER 0 0 0 0 0 0 0 0 10 0 10 0
END
1 molecule converted


Then paste these lines into a new pdb file...


Top
 Profile  
 
Display posts from previous:  Sort by  
Post new topic Reply to topic  [ 2 posts ] 

All times are UTC


Who is online

Users browsing this forum: No registered users and 7 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:  
cron
POWERED_BY
Translated by MaĆ«l Soucaze © 2009 phpBB.fr