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manishi
PostPosted: Sat Dec 12, 2009 6:26 am 
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Dear Vina Users,

I am doing virtual screening using AutoDock Vina. While running Vina on some of the files, the following error statement is given for a number of ligand files

Parse error on line 23 in file "~/Bio_Ligands/LIG_AND2/out_1401.pdbqt": Atom 12 has not been found in this branch

The ligand file is:
Code:
REMARK  5 active torsions:
REMARK  status: ('A' for Active; 'I' for Inactive)
REMARK    1  A    between atoms: O_5  and  C_22
REMARK    2  A    between atoms: C_6  and  C_8
REMARK    3  A    between atoms: C_6  and  C_11
REMARK    4  A    between atoms: C_8  and  C_10
REMARK    5  A    between atoms: C_11  and  C_13
ROOT
HETATM    1  O   LIG     1       4.321   0.965   0.000  1.00  0.00    -0.291 OA
HETATM    2  C   LIG     1       4.989   0.221   0.000  1.00  0.00     0.178 C
ENDROOT
BRANCH   2   3
HETATM    3  C   LIG     1       4.678  -0.730   0.000  1.00  0.00     0.117 A
HETATM    4  C   LIG     1       3.732  -1.034   0.000  1.00  0.00    -0.019 A
HETATM    5  C   LIG     1       3.732  -2.034   0.000  1.00  0.00     0.115 A
HETATM    6  C   LIG     1       2.866  -0.534   0.000  1.00  0.00     0.008 A
HETATM    7  O   LIG     1       4.678  -2.339   0.000  1.00  0.00    -0.363 OA
HETATM    8  C   LIG     1       2.866  -2.534   0.000  1.00  0.00     0.016 A
HETATM    9  C   LIG     1       5.262  -1.534   0.000  1.00  0.00     0.074 A
HETATM   10  C   LIG     1       2.000  -2.034   0.000  1.00  0.00    -0.001 A
HETATM   11  C   LIG     1       2.000  -1.034   0.000  1.00  0.00     0.000 A
BRANCH   9  12
ENDBRANCH   9  12
BRANCH   9  12
HETATM   12  C   LIG     1       6.262  -1.534   0.000  1.00  0.00     0.115 C
HETATM   13  C   LIG     1       6.762  -2.400   0.000  1.00  0.00     0.128 C
ENDBRANCH   9  12
ENDBRANCH   2   3
BRANCH   2  14
HETATM   14  C   LIG     1       5.967   0.427   0.000  1.00  0.00     0.014 A
HETATM   15  C   LIG     1       6.278   1.378   0.000  1.00  0.00     0.033 A
HETATM   16  C   LIG     1       7.257   1.584   0.000  1.00  0.00     0.032 A
HETATM   17 BR   LIG     1       7.567   2.534   0.000  1.00  0.00    -0.079 Br
HETATM   18  C   LIG     1       7.925   0.840   0.000  1.00  0.00     0.177 A
HETATM   19  C   LIG     1       7.614  -0.111   0.000  1.00  0.00     0.021 A
HETATM   20 BR   LIG     1       8.282  -0.855   0.000  1.00  0.00    -0.170 Br
HETATM   21  C   LIG     1       6.635  -0.317   0.000  1.00  0.00     0.052 A
BRANCH  18  22
HETATM   22  O   LIG     1       8.903   1.046   0.000  1.00  0.00    -0.370 OA
HETATM   23  H   LIG     1       9.096   1.635   0.000  1.00  0.00     0.212 HD
ENDBRANCH  18  22
ENDBRANCH   2  14
TORSDOF 5


Kindly guide me how to rectify this problem??..

~Manishi
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oleg_trott
PostPosted: Sun Dec 13, 2009 11:28 pm 
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manishi wrote:
Dear Vina Users,

I am doing virtual screening using AutoDock Vina. While running Vina on some of the files, the following error statement is given for a number of ligand files

Parse error on line 23 in file "~/Bio_Ligands/LIG_AND2/out_1401.pdbqt": Atom 12 has not been found in this branch


You provided a bad PDBQT file. Is the error message not clear and descriptive enough?

_________________
Please do not email or PM me with questions. Vina.scripps.edu/questions.html explains where to find help.
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aravindprasad
PostPosted: Thu Jun 23, 2011 1:45 pm 
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Quite on old thread that I am reviving...

What is the pdbqt file was also generated by PyMOL plugin for AutoDock? I guess the error message is not very descriptive enough then :-)
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goncalojustino
PostPosted: Thu Mar 29, 2012 9:39 am 
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Hi,

I just came across the same very problem today.
I converted my files to pdbqt using prepare_ligand4.py and had a "Parse error on line 44 in file "test.pdbqt": Atom 23 has not been found in this branch" error when running vina.


Any ideas ?
Could it that some molecule type - which ? -cause this ?
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