[Dock-fans] DOCK error in prepare_amber.pl

Scott Brozell sbrozell at scripps.edu
Mon Feb 4 11:53:35 PST 2008


Hi,

On Mon, 4 Feb 2008, snoze pa wrote:

> I do not have any errror message in compiling DOCK. But when I am using it

What about from the tests which involve amber score ?

> it is unable to create lig.1.amber.pdb file using amberscore.pl script. I do

There is no such file amberscore.pl.
Perhaps you mean prepare_amber.pl ?

> not have amber. I read the faq about this error.

And ?
Did you verify that AMBERHOME is not defined ?

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

Scott

> 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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