Re: [AMBER] Vina Docking model is not accepted in Antechamber

From: Aldo Segura <>
Date: Tue, 16 Oct 2012 13:35:43 -0700 (PDT)


You should try to use the "" script included in AutodockTools
(/your_installation/MGLTools-1.5.6rc3/MGLToolsPckgs/AutoDockTools/Utilities24/ If you think something is lost in your pdb, you could send your ligand pdb fileto The PRODRG Server and download the processed pdb file.

Best regards,
Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747

 De: Chris Chris <>
Para: AMBER Mailing List <>
Enviado: Martes, 16 de octubre, 2012 13:47:09
Asunto: [AMBER] Vina Docking model is not accepted in Antechamber
I docked a ligand to a protein using Autodoc Vina. From the resulting .pdbqt file I extracted the model I was interested in, opened it in PyMol, and saved the structure as a .pdb file (see attached). However, when I try to process this .pdb file in antechamber using :

 antechamber -i ctz_101512_100mod1.pdb -fi pdb -o ctz_101512_100mod1.mol2 -fo mol2 -c bcc -s 2

The following error message is produced:

Warning: detected more than 10 Residue sequence numbers;
    this may be a large multiple residue PDB file;
    large multiple residue PDB files are not supported.
    Continuing, but problems may be encountered.
Running: /usr/local/packages/AMBER11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

For atom[10]:O, the best APS is not zero, bonds involved by this atom are frozen

---Judge bond type for Residue 1 with ID of 11 and Name of CTZ ---

Warning: the assigned bond types may be wrong, please : 
(1) double check the structure (the connectivity) and/or 
(2) adjust atom valence penalty parameters in APS.DAT, and/or 
(3) increase PSCUTOFF in define.h and recompile bondtype.c
    Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time

Error: cannot run "/usr/local/packages/AMBER11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit

can anyone point me in the right direction here? Should I not use PyMol to make the pdb file? To convert from PDBQT format to PDB format, the simplest thing to do is to remove the charge (Q) and atom type (T) columns but it seems that PyMol has done this....but maybe lost the proper connect data


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Received on Tue Oct 16 2012 - 14:00:03 PDT
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