[Dock-fans] DOCK error in prepare_amber.pl

Scott Brozell sbrozell at scripps.edu
Fri Feb 1 17:09:45 PST 2008


Hi,

On Fri, 1 Feb 2008, snoze pa wrote:

> I am following this tutorial
> http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm
>
> But I am unable to get the file lig.1.amber.pdb
>
> perl prepare_amber.pl lig.mol2 1lgu.pdb
> Coordinate and parameter files for the Receptor 1lgu generated.
> The AMBER score tagged mol2 file lig.amber_score.mol2 generated.
> Splitting the multiple Ligand mol2 file into single mol2 files.
> The single mol2 files will have the prefix: lig
> Generating coordinate and parameter files with AM1-BCC charges.
> This may be time consuming.
> Ligand lig.1 has total charge 0
> Coordinate and parameter files for the Ligand lig.1 generated.
> Coordinate and parameter files for the Complex 1lgu.lig.1 generated.
> prepare_amber.pl completed.
>
> and when i am running dock then it is unable to find the file
> Initializing Library File Routines...
> getpdb: can't open file lig.1.amber.pdb

Did you
"examine the amberize*.out and *.log files for warnings and errors."
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore

You didn't read the FAQ
http://dock.compbio.ucsf.edu/DOCK_6/faq.htm
or search the dock fans archives:
http://dock.compbio.ucsf.edu/DOCK_6/index.htm
to find
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-September/001218.html

Scott



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