[AMBER] Vina Docking model is not accepted in Antechamber

From: Chris Chris <alpharecept.yahoo.com>
Date: Tue, 16 Oct 2012 11:47:09 -0700 (PDT)

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 Thanks, Chris 

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Received on Tue Oct 16 2012 - 12:00:06 PDT
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