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PostPosted: Thu Jul 09, 2009 8:52 am 
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Hi all,

Upon loading a peptide ligand with AutoDockTools (Ligand-Input-Open ...), I get the error message:
--------
adding gasteiger charges to peptide
GlycoPh_aligned_model:A:THR13:HG1 and GlycoPh_aligned_model:A:THR13:HG1 have the same coordinates ERROR *********************************************
Traceback (most recent call last):
File "C:\Program Files\MGLTools 1.5.4\MGLToolsPckgs\ViewerFramework\VF.py", line 737, in tryto
result = apply( command, args, kw )
File "C:\Program Files\MGLTools 1.5.4\MGLToolsPckgs\AutoDockTools\autotorsCommands.py", line 991, in doit ...
...
File "C:\Program Files\MGLTools 1.5.4\MGLToolsPckgs\PyBabel\util.py", line 48, in bond_angle
(a[2] - b[2]) * (c[2] - b[2]) ) / dist
ZeroDivisionError: float division
-----

Here are the coordinates:

ATOM 203 HG1 THR A 13 34.141 34.375 23.585 1.00 15.00
ATOM 204 HG21 THR A 13 35.234 35.469 22.487 1.00 15.00
ATOM 205 HG22 THR A 13 34.531 36.875 21.592 1.00 15.00
ATOM 206 HG23 THR A 13 34.922 35.313 20.747 1.00 15.00
ATOM 207 N LEU A 14 33.828 38.203 22.720 1.00 15.00


Obviously the same atom SHOULD have the same coordinates. Any idea what to do ?

Many thanks
Andreas
(MGL Tools 1.5.4 Revision 24, Windows XP, Laptop)


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PostPosted: Tue Jul 14, 2009 4:29 pm 
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Hi Andreas,
The atoms in the code snippet which you attached are too far apart for bonds to be built by default.
The lack of bonds lead to this (somewhat obscure) error message.

How were these hydrogens generated?

akukol wrote:
.....
Here are the coordinates:

ATOM 203 HG1 THR A 13 34.141 34.375 23.585 1.00 15.00
ATOM 204 HG21 THR A 13 35.234 35.469 22.487 1.00 15.00
ATOM 205 HG22 THR A 13 34.531 36.875 21.592 1.00 15.00
ATOM 206 HG23 THR A 13 34.922 35.313 20.747 1.00 15.00
ATOM 207 N LEU A 14 33.828 38.203 22.720 1.00 15.00


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PostPosted: Wed Jul 22, 2009 6:57 pm 
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The coordinates were generated as a standard alpha-helix from the amino acid sequence using NOC viewer. They are displayed correctly in RasMol.

Many thanks
Andreas

-------------------
Note added later: Loading the peptide with VegaZZ and saving it as .pdbq saved this problem. Afterwards it could be loaded by AutoDock tools without a problem.


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