Enlighten2

Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems.

To acknowledge the use of the Enlighten2 plugin and/or protocols, please refer to this website. (There is no publication to cite yet, please check back later.)

Aimed at:

• Experimental biochemists/enzymologists interested in gaining detailed insight into protein-ligand / enzyme-substrate complexes.
• Biomolecular researchers that would like to perform simulations in a high(er)-throughput fashion, e.g. for testing and hypothesis generation

Minimal software requirements:

• AmberTools14 or later (the manual - Amber14.pdf or later - has instructions for installation)

Several utitilies/programs from AmberTools14 (or later) are used for the majority of tasks.

Additional recommended software requirements:

• propka31 (see the github site or here: www.propka.ki.ku.dk; Required for pKa estimation titratable residues, in presence of ligand)

###Download the repository on Linux/UNIX/Mac :

First ensure that git is installed. Instructions are here.

Command-line:

1. In the right-hand corner of this page, there is a title "HTTPS clone URL" with a URL in a field below it. Copy this link

2. Go to the command line on your Linux/Mac and cd to a suitable location to create the Repository Then type:

   git clone https://github.com/vanderkamp/enlighten2.git

   On some UNIX clusters, you may need to use SSH rather than HTTPS to clone the repository. This typically means you will also need to add your public ssh key for the cluster (~/.ssh/id_rsa.pub) to your github account here: https://github.com/settings/ssh

   Once the public ssh key is added, you can run:

   git clone [email protected]:vanderkamp/enlighten2.git

3. Prior to running Enlighten through the command line, make sure your environment is set up for the external programs

   For AmberTools, do the following:

   source <full path to amber directory, e.g. /users/me/amber14/>amber.sh

   For PropKa, ensure that propka31 is in your $PATH (i.e. it is recognised as command from the command-line), e.g. in bash:

   export PATH=$PATH:<path to propka>/propka31

Available protocols

PREP: prep.py

prep.py takes enzyme-ligand pdb file and generates ligand parameters, adds hydrogens, adds solvent (sphere), generates Amber topology/coordinate files.

Usage:

prep.py <pdb file> <ligand name> <net ligand charge> [<additional parameters file>]

• The pdb file should contain at least 1 (non-protein) ligand, WITH all hydrogens added!
• Uses the following AmberTools14 programs: antechamber (& sqm), prmchk2, pdb4amber, reduce, tleap
• Ideally requires installation of propka31 (and put in $PATH)