ADL: assertion "finite(avg)" failed

Jack Shultz jackygrahamez at gmail.com
Mon Jan 28 13:19:43 PST 2008


Oh I see it should have been in the path if you copied it to bin. did you
run the prepare scirpts in this order?
1) prepare_ligand4.py -l ligand_name
2) prepare_receptor4.py -r receptor_name
3) prepare_gpf4.py -l ligand_name -r receptor_name
4) prepare_dpf4.py -l ligand_name -r receptor_name

Then run

autogrid -p Grid_parameterfile (*.gpf)
autodock -p Autodock_parameterfile (*.dpf)

Jack
On Jan 28, 2008 3:51 PM, Jack Shultz <jackygrahamez at gmail.com> wrote:

> Instead of moving everything around...have you tried setting the path so
> you can execute autodock4.exe anywhere in Cygwin?
> $ PATH=$PATH:/usr/src/autodocksuite-4.0.1/bin/i86Cygwin
> You will need to update your shell configuration like bash
> /etc/bash.bashrc
> Jack
>
> On Jan 28, 2008 3:28 PM, Antonio Cavazzuti <acavazzuti at ipb.csic.es> wrote:
>
> > Hi,
> > I work under Cygwin installed on Windows XP. I prepare ligand and
> > receptor
> > using ADT 1.5 , I move output files to autogrid4.exe folder and I start
> > the
> > job from the command line. I move output files to ADT folder and I
> > obtain
> > .dpf. I finally move the .dpf file in the directory
> > c:/cygwin/usr/local/bin
> > where autodock4.exe is and I start autodock4 job from command line.
> > Autodock4 hangup after 20' (pentium4 2Ghz) with following message:
> >
> > assertion "finite(avg)" failed: file "gs.cc", line855
> >       8 [sig] autodock4 3884 C:\cygwin\usr\local\bin\autodock4.exe: ***
> > fatal
> > error - called with threadlist_ix -1
> > Hangup
> >
> > How solve this problem?
> >
> > Before reaching this point, I had to correct .dpf file that was looking
> > for a
> > "_rigid.A.map" (this map was not generated by autogrid4), by deleting
> > the
> > correspondent line. Maybe this is the cause of previous problem?
> >
> > Somebody can indicate me how avoid to skip from autodock folder to ADT
> > folder
> > cutting and pasting files?
> >
> > To conclude, somebody can indicate me how correctly locate Cygwin,
> > Python2.5,
> > ADT 1.5 and Autodock4/Autogrid4 folders under WinXP, and what is the
> > corret
> > installing sequence?
> >
> > Thank you
> > Antonio
> >
> >
> >
> > Instituto de Parasitologia y Biomedicina "Lopez-Neyra"
> > Avda. Conocimiento S/N
> > Parque Tecnologico Ciencias de la Salud
> > 18100 Armilla - GRANADA
> > Spain
> > Tlf: 958181621
> > Fax: 958181632
> > http://www.ipb.csic.es
> > --
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
>
>


More information about the autodock mailing list