[Dock-fans] Help request

Arturo Rojo ard at xanum.uam.mx
Tue Mar 1 17:05:11 PST 2005

Dear friends,

I am a former user of DOCK4, installing DOCK5.1.1. I have some questions
about it, and I would be very grateful if someone could help me.

First, when I run (in linux) the demo several times I always get the same
results, but with DOCK4 I remember to get slightly different scores in each 
run due to the random orientation algorithm. Is something wrong with my 
installation?  Interestingly, results are the same when run in the same
computer but different to those run in other processor with the same
random_number_seed. Also (as expected) running DOCK5 with different
random_number_seed in the same computer produces different scoring.

Second, I have installed Cygwin for executing the windows binary but I
do not know how to run DOCK on this emulator. Do you know where can I find 
a manual for the windows version? I tried:
source dock5_windows.exe
and I got:
bash: MZ?: command not found

Finally, the posibility of multiprocessor runs with DOCK5.1.1 is mentioned
in the documentation, but there is a README file stating that it is not
ready yet. Do you know if now there is an available parallel version of DOCK5?

Thank you in advance for your kind help.


            Arturo Rojo-Domínguez.
            Depto. de Química. Área de Biofisicoquímica. Lab. R-209.
            Universidad Autónoma Metropolitana-Iztapalapa.
            San Rafael Atlixco 186. 09340 México, D.F.
            Tel. +52 (55) 58044674. Fax. 58044666

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