Getting started with DOCK 3.7: Difference between revisions
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= Acquire our software = | = Acquire our software = | ||
Here we are installing a private copy under a single user account. It is easy to change this to a global location, e.g. /nfs/software . You can request a license and a copy (free to academics, a | Here we are installing a private copy under a single user account. It is easy to change 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 [http://dock.compbio.ucsf.edu/Online_licensing/dock_license_application.html http://dock.compbio.ucsf.edu/Online_licensing/dock_license_application.html]. Request [[DOCK 3.7]]. | ||
cd | cd | ||
mkdir code | mkdir code | ||
cd code | cd code | ||
cp ~xyz/DOCK.tgz . # or get distro from dock website | cp ~xyz/DOCK.tgz . # or get distro from dock.compbio.ucsf.edu website as above | ||
tar xzf DOCK.tgz # unpack | tar xzf DOCK.tgz # unpack | ||
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= Perform your first docking from PDB code alone using be_blasti = | = Perform your first docking from PDB code alone using be_blasti = | ||
* run be_blasti | |||
* run blastermaster | |||
= Perform your first fine tuned docking run = | = Perform your first fine tuned docking run = | ||
In this docking run, we are going to make adjustments from the default protocol in several areas: | |||
* the docking spheres or hot-spots | |||
* the vdw grids | |||
* the electrostatics grids | |||
* the size of the box | |||
* a zinc ion and its coordinating residues | |||
= Get a pre-prepared library = | = Get a pre-prepared library = | ||
[[DOCK 3.7]] uses a format new to this version of [[DOCK]] called [mol2db2 format]]. It will be available via the normal channels in ZINC. You can of course also prepare your own version locally. As of this writing, you can currently get pre-prepared subsets of lead-like and fragment-like from our server (details to go here). | |||
Return to [[DOCK 3.7]]. | Return to [[DOCK 3.7]]. |
Revision as of 18:40, 23 February 2014
You want to install DOCK 3.7 on your own system. These are the notes I made while doing it. These are just recommendations, based on my experience. You are free to simply download the software and experiment!
Acquire 3rd party software
- Recommend Centos 6.3 or higher, but other unixes should work
- python 2.7 series - We do not support the 3.x series, and 2.6 or earlier can also cause problems.
- amsol - for database building
- omega / OpenEye - for database building
Acquire our software
Here we are installing a private copy under a single user account. It is easy to change 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 http://dock.compbio.ucsf.edu/Online_licensing/dock_license_application.html. Request DOCK 3.7.
cd mkdir code cd code cp ~xyz/DOCK.tgz . # or get distro from dock.compbio.ucsf.edu website as above tar xzf DOCK.tgz # unpack
set up .cshrc (or .bashrc)
You need to create something like this, depending on your exact circumstances.
setenv DOCKBASE /raid4/people/mattchu/code/DOCK setenv SOFT /raid3/software setenv ENV_PYTHON "$SOFT/python/bin/python-env.csh 2.7" source $ENV_PYTHON set path = ($path $DOCKBASE/bin)
Test the installation using the built-in test scripts
cd $DOCKBASE/test ./all-test.sh
Perform your first docking with pre-prepared files
cd mkdir -p docking/test1 cd $DOCKBASE/test/data/xiap/proteins/initial cp rec.pdb xtal-lig.pdb ~/docking/test1/ cd ~/docking/test1/ blastermaster.py -v
Perform your first database generation, using endogenous human metabolites
cd mkdir -p database/testa cd database/testa wget http://zinc.docking.org/db/byvendor/hmdbendo/hmdbendo_p0.smi.gz gunzip hmdbendo_p0.smi.gz *dbgen.csh
Perform your first docking from PDB code alone using be_blasti
- run be_blasti
- run blastermaster
Perform your first fine tuned docking run
In this docking run, we are going to make adjustments from the default protocol in several areas:
- the docking spheres or hot-spots
- the vdw grids
- the electrostatics grids
- the size of the box
- a zinc ion and its coordinating residues
Get a pre-prepared library
DOCK 3.7 uses a format new to this version of DOCK called [mol2db2 format]]. It will be available via the normal channels in ZINC. You can of course also prepare your own version locally. As of this writing, you can currently get pre-prepared subsets of lead-like and fragment-like from our server (details to go here).
Return to DOCK 3.7.