Difference between revisions of "Install DOCK 3.7"

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(Created page with "= 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 ...")
 
(Installing third-party softwares)
 
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= Timeline =
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If you do not already have a cluster with middleware, see: [[So you want to set up a lab]].
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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{{TOCright}}
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'''Now you are ready for the installation'''
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= Installing third-party softwares =
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Currently needed third party software:
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* OpenEye (OEChem, Omega)
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** More information [http://www.eyesopen.com/oechem-tk here for OEChem TK]
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** More information  [http://www.eyesopen.com/omega here for Omega]
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Apply for academic license  [http://www.eyesopen.com/academic here]
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* JChemBase (Chemaxon)
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** Definitely need marvin, molconvert, molcharge . . .
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** Academic license [http://www.chemaxon.com/my-chemaxon/my-academic-license/ here]
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* Corina ([https://www.mn-am.com/products/corina here])
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* [http://www.cgl.ucsf.edu/chimera/ Chimera]
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* AMSOL
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** A '''modified''' version of AMSOL6.5.3 is required for DOCK 3.5.54, 3.6, and 3.7
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** [http://comp.chem.umn.edu/amsol/ AMSOL7.1] is need for DOCK 3.7.1. For install and path instruction, see [[AMSOL]]
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*PYTHON
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**numpy
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**scipy
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**matplotlib
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**biopython (this is need for only one or two scripts, beblasti.py )
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** virtual environments are very helpful.
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**see $DOCKBASE/install/environ/python/requirements.txt for more information.
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* RDkit (not required but useful, see  $DOCKBASE/install/environ/python/rdkit.sh for help building rdkit.)
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* msms (only need for using beblasti.py) see [[installing msms]]
  
= Hardware and Operating System =
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The DOCK Environment is a collection of scripts, programs and 3rd party programs.
* 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 =
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[[Compbio middleware]] needed to support our software and a computational pharmacology lab.
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= Our software =
 
= Our software =
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[http://dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html]
 
[http://dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html]
  
  mkdir -p ~/code/DOCK
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  mkdir -p ~/code
  cd ~/code/DOCK
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  cd ~/code
  tar xzf dock3.7.tgz
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  tar xzf dock37_source.tar.gz
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ln -s dock-3.7-release DOCK
  
 
= set up .cshrc  (or .bashrc equivalent) =
 
= set up .cshrc  (or .bashrc equivalent) =
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= Test 1: Basic tests =  
 
= 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.
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Before you test our software, test that all third party software is correctly installed.
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cd ~/$DOCKBASE/test
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./third-party-test.sh
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This will tell you quick what you forgot to install or if there is any obvious problem with your installation. Once the above works without error, you are ready to test our software.  
 
  cd ~/$DOCKBASE/test
 
  cd ~/$DOCKBASE/test
 
  ./all-test.sh
 
  ./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.  
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This should run about 10-30 minutes depending on your hardware.
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If you can pass the tests without error, congratulations! You are ready to get started with docking: [[Getting started with DOCK 3.7]].
 +
 
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== Possible problems and solutions during installation ==
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* OpenEye missing or problem
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* Python missing or problem
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* AMSOL missing or problem
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* Chemaxon missing or problem
  
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* SGE or problem
  
 
[[Category:Sysadmin]]
 
[[Category:Sysadmin]]
 
[[Category:DOCK 3.7]]
 
[[Category:DOCK 3.7]]
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[[Category:Setup]]

Latest revision as of 12:32, 25 March 2019

If you do not already have a cluster with middleware, see: So you want to set up a lab.

Now you are ready for the installation

Installing third-party softwares

Currently needed third party software:

Apply for academic license here

  • JChemBase (Chemaxon)
    • Definitely need marvin, molconvert, molcharge . . .
    • Academic license here
  • Corina (here)
  • Chimera
  • AMSOL
    • A modified version of AMSOL6.5.3 is required for DOCK 3.5.54, 3.6, and 3.7
    • AMSOL7.1 is need for DOCK 3.7.1. For install and path instruction, see AMSOL
  • PYTHON
    • numpy
    • scipy
    • matplotlib
    • biopython (this is need for only one or two scripts, beblasti.py )
    • virtual environments are very helpful.
    • see $DOCKBASE/install/environ/python/requirements.txt for more information.
  • RDkit (not required but useful, see $DOCKBASE/install/environ/python/rdkit.sh for help building rdkit.)
  • msms (only need for using beblasti.py) see installing msms

The DOCK Environment is a collection of scripts, programs and 3rd party programs.

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
cd ~/code
tar xzf dock37_source.tar.gz
ln -s dock-3.7-release DOCK

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

Before you test our software, test that all third party software is correctly installed.

cd ~/$DOCKBASE/test
./third-party-test.sh

This will tell you quick what you forgot to install or if there is any obvious problem with your installation. Once the above works without error, you are ready to test our software.

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

This should run about 10-30 minutes depending on your hardware. If you can pass the tests without error, congratulations! You are ready to get started with docking: Getting started with DOCK 3.7.

Possible problems and solutions during installation

  • OpenEye missing or problem
  • Python missing or problem
  • AMSOL missing or problem
  • Chemaxon missing or problem
  • SGE or problem