AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber prep question

From: case (
Date: Thu Jul 09 2009 - 10:16:17 CDT

On Thu, Jul 09, 2009, Andrew Olson wrote:

> [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
> judgebondtype() of antechamber.c properly, exit

Can you post the atp_H_1.pdb file you use as input? We need to be able to
reproduce the problem in order to make progress.


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