Getting started

Click here to download a tarball containing all of the input files that will be needed for this workshop. The file is called ligandswap.tgz. Once you have downloaded the file, change into the directory that you downloaded it into and unpack it by typing;

tar -zxvf ligandswap.tgz

This will create a new directory called ligandswap. Change into this directory and list its contents by typing;

cd ligandswap
ls

You should see a list of files that looks something like this;

README        config      cti_gas.crd    cti_gas.pdb
cti_gas.top   fmc.30.crd  rec_fmc.pdb    rec_fmc.top

We will be using the ligandswap program that comes with the Sire Molecular Simulation Framework to run the simulations in this part of the workshop. You will need to be using at least Sire version 2016.2 or newer. You can check the version by typing;

$SIRE/bin/ligandswap --version

If Sire has been installed, you should see something like this printed to the screen;

Starting /path/to/sire.app/bin/ligandswap: number of threads equals 4

ligandswap version 1.0 implemented using
Sire 2016.2.0 [c++15|48abdec, clean]

If you do, then Sire is installed correctly, and you can continue to the next part of the workshop.

If you don’t, then you need to download and install Sire. You can do this by following the instructions on this page. This will install Sire into your home directory. Once you have installed Sire, you need to set the $SIRE environment variable to point to this installation directory. You can do this by typing;

export SIRE=$HOME/sire.app

Now, try typing

$SIRE/bin/ligandswap --version

This should print out the version of ligandswap, showing similar output to above. You are now ready to continue to the next part of the workshop. If you don’t see something similar to the above output, then please ask for help or .

Note - Sire 2016.2 is planned to be released by the end of June 2016. Please be patient while we finalise this release. In the interim, please download a pre-release from here

and then type chmod a+x sire_2016*.run ; ./sire_2016*.run to install it


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