[Dock-fans] Run "prepare_amber.pl lig.mol2 1lgu.pdb" err!

[Scott Brozell]

Hi,

On Thu, 12 Mar 2009, li bai wrote:

> I use the "Structure Preparation & AMBER Score"of the tutor, but in the dock6.2. when I "input:prepare_amber.pl lig.mol2 1lgu.pdb". I get the err as below:
> "
> Using receptor file prefix: 1lgu
> Using ligand file prefix: lig.1
> Error: the input file, lig.1.gaff.mol2, does not exist !
> "

These lines are from amberize_complex.out.
The last one indicates an error during amberize_ligand
which is called by prepare_amber.pl.
Examine amberize_ligand.out to determine the source of the error.

Scott