AMBER Archive (2009)

Subject: [AMBER] Antechamber prep question

From: Andrew Olson (
Date: Thu Jul 09 2009 - 09:39:25 CDT

I have perused the archives and found similar topics but i still cant figure this out.  I have a ligand that was docked using Autodock and im now attempting to insert into the receptor to run some MD on it.  So im trying to correct the atom types and charges using antechamber.  I am following the basic tutorial on antechamber so im attempting to convert my pdb to mol2 but i get this error that alot of people are getting;
[pcp]:Research/AMBER/ATP] NAME% $AMBERHOME/bin/antechamber -i atp_H_1.pdb -fi pdb -o ATP.mol2 -fo mol2 -c bcc
For atom[7]:O5, the best APS is not zero, bonds involved by this atom are frozen
The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8 (aromatic double)Error: cannot run "/usr/local/Amber10/amber10/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit
I add H's everywhere and charges (Not sure if that is necessary) using chimera and run the same command and i get;
4 is not a valid atom id in CONECT    4   22    5    2   40

Not sure where to go from here.  Many thanks

AMBER mailing list