AMBER Archive (2006)

Subject: Re: AMBER: a ligand file

From: David A. Case (
Date: Wed Sep 06 2006 - 16:40:30 CDT

On Wed, Sep 06, 2006, Fenghui Fan wrote:

> I can add the H to the cAMP.pdb and save it into
> another pdb file. However Antechamber still cannot
> work with the new pdb file, the reason and the error
> message is same as previous e-mail to you:
> Error: cannot run "/home/local/amber9/exe/bondtype -i
> -f ac -j full" in judgebondtype () of antechamber.c
> properly, exit.
> Will you please tell me how to solve this problewm?

No one can help without being able to see the pdb file you are giving to
antechamber. Be sure to check visually that you have the correct hydrogen
positions; if you have a charged molecule, be sure to use the "-nc" flag
in antechamber to provide that information.


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