[Dock-fans] DOCK error in prepare_amber.pl

snoze pa snoze.pa at gmail.com
Mon Feb 4 09:16:57 PST 2008


I do not have any errror message in compiling DOCK. But when I am using it
it is unable to create lig.1.amber.pdb file using amberscore.pl script. I do
not have amber. I read the faq about this error.



On Feb 1, 2008 7:09 PM, Scott Brozell <sbrozell at scripps.edu> wrote:

> 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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