AMBER Archive (2006)

Subject: Re: AMBER: ligand file

From: David A. Case (
Date: Mon Sep 04 2006 - 14:02:34 CDT

On Mon, Sep 04, 2006, Fenghui Fan wrote:
> When I use ANTECHAMBER to get the prepin file,
> ANTECHAMBER says the bondtype cannot be run. Will you
> tell me what should I do in oreder to get the cAMP
> prepin file.

1. As previously requested, please give the *exact* error message(s) when
reporting problems.

2. Antechamber requires input files with all hydrogens present; your file
just has heavy atoms, so you will have to manually add the necessary
hydrogens, for example using xleap.


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