[Dock-fans] docking on a linux cluster

Jose A zyclopia at gmail.com
Fri Jul 22 10:54:28 PDT 2005

Hello everybody,

I have some questions...

1) has DOCK been developed on other platforms (windows, linux, mac) to
the same extent as for UNIX? would you say DOCK runs for Mac as
smoothly as it does for UNIX? or is the UNIX version constantly
"ahead" of the others?

2) I noticed that in the demo scripts DOCK is set up with energy
scoring both for primary AND secondary scoring. is this the recomended
combo? I used to score with contact score primary and energy as
secondary. is this better or worse? or does it vary from target to
target? After reading the manual a couple of times, it is still not
clear to me how setting up one scoring function as primary or
otherwise makes any difference. If anybody cares to educate me I would
be grateful...

3) It seems there is at least another person having a similar problem
to mine when trying to use DOCK on a linux cluster. I can run the demo
fine. I can change some keywords to my liking without problems (such
as turning on the bump filter and switching automated matching
off)...but as soon as I switch to a database
with a few hundred molecules DOCK scores a few and then gets stuck and
kills itself (without warning). Rerunning repeats the process with
DOCK failing at the same molecule. Removing the "bad" molecule allows
DOCK to go farther down the list, but it gets stuck again at some
other molecule later. The mol2 file seems to be ok (zinc#267). How
could I begin to troubleshoot this???? can I assume grid and cluster
files are "OK" since a single molecule runs fine?  finally, I have to
say so far I hadn't had this problem on an SGI workstation...should I
run DOCK with dock5.linux on the cluster instead of dock5.mpi? or that
wouldn't make a difference?

Thanks for giving this any thought,


PS: here is a copy of the PBS script I am using to run dock. If you
think it is missing something let me know...

#!/bin/csh -f
#PBS -N dock_only
#PBS -o dock_only.out
#PBS -e dock_only.err
#PBS -m abe
#PBS -M my email address goes here
#PBS -q submit
#PBS -l nodes=2:ppn=1
set path = ($path /opt/lam/icc/bin)
set MPIRUN = mpirun

setenv LD_LIBRARY_PATH /opt/lam/icc/lib:/opt/intel/cc81/lib


echo Running dock_only...

# Regenerate ligand:receptor complex with flexible ligand
set EXE = /apps/dock/dock52/bin/dock5
cd /home/jahp/demo/4_dock
mpirun -np 2 $EXE -i dock.in -o dock.out

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