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 Post subject: Error message
PostPosted: Mon Jul 12, 2010 6:02 pm 

Joined: Fri Apr 09, 2010 7:37 pm
Posts: 8
Hi,
I would like to know why I receive next message

Current processing component(s):
Refresh status

Create Protein maps – error The error message:
tools/autogrid5: ERROR: The number of atom types found in the receptor PDBQT (7) does not match the number specified by the "receptor_types" command (6) in the GPF!
tools/autogrid5: ERROR: Sorry, AutoGrid cannot continue.


What am I doing wrong setting simulation box?
Thanks a lot.

Lola


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 Post subject: Re: Error message
PostPosted: Tue Jul 13, 2010 7:16 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
Dear Lola,

please select "Gasteiger" as a partial charge calculation method in the Protein clean window for this protein. Quantum mechanical charge calculation (Mozyme) is much more sensible and fails more often.

Kind Regards,
Zsolt

Loadeanda wrote:
Hi,
I would like to know why I receive next message

Current processing component(s):
Refresh status

Create Protein maps – error The error message:
tools/autogrid5: ERROR: The number of atom types found in the receptor PDBQT (7) does not match the number specified by the "receptor_types" command (6) in the GPF!
tools/autogrid5: ERROR: Sorry, AutoGrid cannot continue.


What am I doing wrong setting simulation box?
Thanks a lot.

Lola


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 Post subject: Re: Error message
PostPosted: Mon May 07, 2012 1:25 pm 

Joined: Mon Apr 16, 2012 6:50 pm
Posts: 4
I was trying to upload my protein and gave me this error message
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 61, in addHydrogens
babel.assignHybridization(mol.allAtoms)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/PyBabel/atomTypes.py", line 127, in assignHybridization
a.babel_atomic_number = self.get_atomic_number(a.babel_type)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/PyBabel/atomTypes.py", line 102, in get_atomic_number
raise ValueError( "Could not find atomic number for %s %s"%
ValueError: Could not find atomic number for Ap Ap

my proteine name 1GL3_M0_P0_site


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 Post subject: Re: Error message
PostPosted: Tue May 08, 2012 7:17 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
In your pdb files there are lines where the atom name is "Ap". Please correct this error and upload your protein again.

pharmaco19 wrote:
I was trying to upload my protein and gave me this error message
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 61, in addHydrogens
babel.assignHybridization(mol.allAtoms)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/PyBabel/atomTypes.py", line 127, in assignHybridization
a.babel_atomic_number = self.get_atomic_number(a.babel_type)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/PyBabel/atomTypes.py", line 102, in get_atomic_number
raise ValueError( "Could not find atomic number for %s %s"%
ValueError: Could not find atomic number for Ap Ap

my proteine name 1GL3_M0_P0_site


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