ADL: Raccoon

Stefano Forli forli at scripps.edu
Mon Mar 8 11:22:39 PST 2010


Dear Pawan,

be sure that the binaries are in the path you specified:

  /cygdrive/c/cygwin/usr/local/bin/i86Cygwin/autodock4

Test it by executing that line in your Cygwin bash shell.

Moreover, please try to follow the instructions reported here:

  http://autodock.scripps.edu/downloads/faqs-help/faq/installing-autodock-on-windows

to test if the installation was successful.
Concerning the "lot of emails" you posted and the answers you didn't get from me, I would 
like to inform you that I have not received any communications from you either personal or 
on the mailing list.

I invite you to read about the netiquette:
http://mgldev.scripps.edu/forum/viewtopic.php?f=23&t=26

Hope this helps,

Stefano



pawan raghav wrote:
>  Dear Forli,
> 
>     I am using Autodock from 2008 and I have posted lot of mails on this but
> I don't get any response from your side. So Please solve my problem as I am
> in need. My problem is about the raccoon that when executing ./RunVS.sh or
> bash ./RunVS.sh it showed an error i.e. nError: the file [$AUTODOCK] doesn't
> exist or is not executable\n. I am using autodock on windows by using
> cygwin. I have installed all the files in
> /cygdrive/c/cygwin/usr/local/bin/i86Cygwin/Bcl_2 directory and autodock.exe
> file in =/cygdrive/c/cygwin/usr/local/bin/i86Cygwin/autodock4 directory. so
> please tell me how to specified correct path in
> export AUTODOCK= "------------------".
> 
> 
> *RunVS.sh*
> 
> ### Generated by AutoDock Raccoon
> 
> export AUTODOCK=/cygdrive/c/cygwin/usr/local/bin/i86Cygwin/autodock4
> 
> type $AUTODOCK &> /dev/null || {
> 
> echo -e "\nError: the file [$AUTODOCK] doesn't exist or is not
> executable\n";
> 
> echo -e "Try to specify the full path to the executable of the AutoDock
> binary in the $0 script";
> 
> echo -e "( i.e. export AUTODOCK=/usr/bin/autodock4 )\n\n";
> 
> echo -e " [ virtuals screening aborted]\n"
> 
> exit 1; }
> 
> export AUTOGRID=C:/cygwin/usr/local/bin/i86Cygwin/autogrid4
> 
> type $AUTOGRID &> /dev/null || {
> 
> echo -e "\nError: the file [$AUTOGRID] doesn't exist or is not
> executable\n";
> 
> echo -e "Try to specify the full path to the executable of the AutoGrid
> binary in the $0 script";
> 
> echo -e "( i.e. AUTOGRID=/usr/bin/autogrid4 )\n\n";
> 
> echo -e " [ virtuals screening aborted]\n"
> 
> exit 1; }
> 
> echo ' ________________________________________________________________'
> 
> echo '
> __________//___________________________/////___________________/____________'
> 
> echo '
> _________/__/__________________________/____/__________________/____________'
> 
> echo '
> ________/____/___________/_____________/_____/_________________/____________'
> 
> echo '
> ________/____/__/_____/_/////___/////__/_____/__/////___/////__/___/________'
> 
> echo '
> _______/______/_/_____/__/_____/_____/_/_____/_/_____/_/_____/_/_//_________'
> 
> echo '
> _______////////_/_____/__/_____/_____/_/_____/_/_____/_/_______//_/_________'
> 
> echo '
> _______/______/_/____//__/___/_/_____/_/____/__/_____/_/_____/_/___/________'
> 
> echo '
> _______/______/__////_/___///___/////__/////____/////___/////__/____/_______'
> 
> echo ' ________________________________________________________________'
> 
> echo ' ______ '
> 
> echo ' / \ '
> 
> echo ' / \ '
> 
> echo ' / \ Raccoon'
> 
> echo ' \ /\ / Virtual '
> 
> echo ' \ / \ / Screening '
> 
> echo ' \/ /\ \/ Generation '
> 
> echo ' /\ \ '
> 
> echo ' /\ \__\ version 1.0b '
> 
> echo ' / \__\ '
> 
> echo ' /____\ '
> 
> echo -e "\n == Press ENTER to start the calculation =="
> 
> read X
> 
> echo 'Docking 5-9_Bcl_2'
> 
> cd 5-9_Bcl_2
> 
> ./run.sh
> 
> cd ..
> 
> echo 'Docking 7-11_Bcl_2'
> 
> cd 7-11_Bcl_2
> 
> ./run.sh
> 
> cd ..
> 
> echo 'Docking 10-14_Bcl_2'
> 
> cd 10-14_Bcl_2
> 
> ./run.sh
> 
> cd ..
> 
> echo 'Docking 9-13_Bcl_2'
> 
> cd 9-13_Bcl_2
> 
> ./run.sh
> 
> cd ..
> 
> echo 'Docking 4-8_Bcl_2'
> 
> cd 4-8_Bcl_2
> 
> ./run.sh
> 
> cd ..
> 
> echo 'Docking 1-5_Bcl_2'
> 
> cd 1-5_Bcl_2
> 
> ./run.sh
> 
> cd ..
> 
> echo 'Docking 8-12_Bcl_2'
> 
> cd 8-12_Bcl_2
> 
> ./run.sh
> 
> cd ..
> 
> echo 'Docking 6-10_Bcl_2'
> 
> cd 6-10_Bcl_2
> 
> ./run.sh
> 
> cd ..
> 
> echo 'Docking 2-6_Bcl_2'
> 
> cd 2-6_Bcl_2
> 
> ./run.sh
> 
> cd ..
> 
> echo 'Docking 11-15_Bcl_2'
> 
> cd 11-15_Bcl_2
> 
> ./run.sh
> 
> cd ..
> 
> echo 'Docking 3-7_Bcl_2'
> 
> cd 3-7_Bcl_2
> 
> ./run.sh
> 
> cd ..
> 
> echo 'Calculation completed.'
> 
> read X
> 
> 


-- 
  Stefano Forli, PhD

  Research Associate
  Olson Molecular Graphics Laboratory
  Dept. Molecular Biology,  MB-5
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

     tel: (858) 784-2055
     fax: (858) 784-2860
     email: forli at scripps.edu
     http://www.scripps.edu/~forli/


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