Here are some cool scripts I've found useful. I've tried to make them usable on many different platforms by creating a Makefile.def file that houses all the paths for various files and folders. Inside this file you'll also find some paths that currently work on Stampede. You should just be able to change the paths inside this file and it should work across all the scripts.

You can use Makefile.def.stampede for stampede or Makefile.def.lonestar for either machine.

Run

make

to compile a few programs, and also check the environment for the existence of necessary ones.

Please note: if you should choose to copy/move one of these scripts into a different folder, you should know that the script will likely break. Most of these are meant to be run from another folder. Something like:

export SCRIPT_DIR=/path/to/script/dir
$SCRIPT_DIR/getTotalEnergy.sh protein.pdb

In addition, many of the scripts are not well-suited for running from a folder other than the folder the input is in. This includes things like runSingles, runAmber, etc.

In order to run docking protocols, you will need at minimum for the following programs to be valid in Makefile.def:

• MolSurf
• MolEnergy (or GPUEnergy, but stick with MolEnergy unless you like cursing the compiler)
• F2Dock_refactored
• PDB2PQR
• TMAlign
• SCWRL4
• PyMol
• OBabel

In particular, you do not need MGLTools--any indication from the program that you do indicated that you probably compiled the wrong version or with the wrong flags.