AMBER Archive (2009)

Subject: [AMBER] Antechamber: stuck at bondtype

From: Jack Shultz (
Date: Wed Jun 17 2009 - 07:50:11 CDT

I am trying to convert a pdb file to mol2 using antechamber. The
example from the tutorial 5 seems to work ok (sustiva.pdb)
The current pdb I am trying to convert just gets stuck at the
bondtype. There are about 110 residues in this protein. It was derived
from a docking complex using Autodock Tools. For testing purposes I
also tried antechamber on the original pdb file used as the receptor
and that had the same issue.

[boincadm_at_vps receptor]$ antechamber -fi pdb -i
receptor_ligand_0.pdbqt -fo mol2 -o receptor_ligand_0.mol2 -s 2

The atom number exceeds the MAXATOM, reallocate memory
Info: the bond number exceeds MAXBOND, reallocate memory automatically
Running: /usr/local/antechamber-1.27/exe/bondtype -i


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