Difference between revisions of "Install DOCK 3.7"

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= Timeline =
 
Once you have all the software and hardware, you can get up and running at a basic level in less than a day. If you do not have all the software, plan for a few days of work. If you've never had your own molecular docking lab, plan for at least a week to learn the basics (and a lifetime to master).  Once you have a basic installation running, plan for a few days to [[get a queuing system working]] the way you like it.  We may be able to help. Ask us, but please read this wiki first.
 
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= Hardware and Operating System =
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1. [[So you want to set up a lab]]
* O/S: We recommend [[Centos]].  
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* Hardware: We recommend Intel or AMD.  [[Supported platforms for DOCK 3.7]].
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= Middleware =
 
[[Compbio middleware]] needed to support our software and a computational pharmacology lab.
 
  
 
= Our software =
 
= Our software =

Revision as of 00:40, 13 March 2014


1. So you want to set up a lab


Our software

Here we install a private copy under a user's account. It is easy to generalize this to a global location, e.g. /nfs/software . You can request a license and a copy (free to academics, a bargain for for-profits) at dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html

mkdir -p ~/code/DOCK
cd ~/code/DOCK
tar xzf dock3.7.tgz

set up .cshrc (or .bashrc equivalent)

You need to create something like this, depending on your exact circumstances.

setenv DOCKBASE /raid4/people/mattchu/code/DOCK
set path = ($path $DOCKBASE/bin)
setenv AMSOLEXE $DOCKBASE/bin/amsol-mod4
setenv OE_DIR /raid3/software/openeye/current
alias pymol ~/pymol/pymol
if ( $?PYTHONPATH ) then
   if ( `echo $PYTHONPATH | grep -c 'openeye/python'` == 0 ) then
       setenv PYTHONPATH $OE_DIR/python:${PYTHONPATH}
   endif
else
   setenv PYTHONPATH $OE_DIR/python
endif

Test 1: Basic tests

This will tell you quick what you forgot to install or if there is any obvious problem with your installation. If you can pass the tests, you are ready to proceed to the following steps.

cd ~/$DOCKBASE/test
./all-test.sh

This should run about 10-30 minutes depending on your hardware, and should either produce clear error messages (work needed) or a clear message that the tests succeeded without problems.