The Schrodinger molecular modeling software suite includes a number of popular programs focused on drug design and materials science but of general applicability, for example Glide, Jaguar, and MacroModel. Maestro is the graphical user interface for the suite. It allows the user to construct and graphically manipulate both simple and complex chemical structures, to apply molecular mechanics and dynamics techniques to evaluate the energies and geometries of molecules in vacuo or in solution, and to display and examine graphically the results of the modeling calculations.
Availability and Restrictions
Versions
The Schrodinger suite is available on Owens. The versions currently available at OSC are:
| Version | Owens |
|---|---|
| 15 | X |
| 16 | X |
| 2018.3 | X |
| 2019.3 | X |
| 2020.1 | X* |
You can use module spider schrodinger to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.
Access
Schrodinger is available to all academic users.
To use Schrodinger you will have to be added to the license server first. Please contact OSC Help to be added. Please note that if you are a non-OSU user, we need to send your name, contact email, and affiliation information to Schrodinger in order to grant access. Currently, we have license for following features:
CANVAS_ELEMENTS CANVAS_MAIN CANVAS_SHARED COMBIGLIDE_MAIN EPIK_MAIN FFLD_OPLS_MAIN GLIDE_MAIN GLIDE_XP_DESC IMPACT_MAIN KNIME_MAIN LIGPREP_MAIN MAESTRO_MAIN MMLIBS MMOD_CONFGEN MMOD_MACROMODEL MMOD_MBAE QIKPROP_MAIN
You need to use one of following software flags in order to use the particular feature of the software without license errors.
macromodel, glide, ligprep, qikprop, epik
You can add -L glide@osc:1 to your job script if you use GLIDE for example. When you use this software flag, then your job won't start until it secures available licenses. Please read the batch script examples below. You can check your license usage via the license usage checking tool.
Publisher/Vendor/Repository and License Type
Schrodinger, LLC/ Commercial
Usage
Usage on Owens
To set up your environment for schrodinger load one of its modulefiles:
module load schrodinger/2019.3
Using schrodinger interactively requires an X11 connection. Typically one will launch the graphical user interface maestro. This can be done with either software rendering:
maestro -SGL
or with hardware rendering:
module load vglrun
vglrun maestro
Note that hardware rendering requires a node with a GPU as well as the additional vglrun syntax above. In principle hardware rendering is superior; however, in practice it can be laggier, and thus software rendering can yield a better experience.
Here is an example batch script that uses schrodinger non-interactively via the batch system:
#!/bin/bash
# Example glide single node batch script.
#SBATCH --job-name=glidebatch
#SBATCH --time=1:00:00
#SBATCH --nodes=1 --ntasks-per-node=28
#SBATCH -L glide@osc:1
module load schrodinger
cp * $TMPDIR
cd $TMPDIR
host=`srun hostname|head -1`
nproc=`srun hostname|wc -l`
glide -WAIT -HOST ${host}:${nproc} -NJOBS 40 receptor_glide.in
ls -l
cp * $SLURM_SUBMIT_DIR
The glide command passes control to the Schrodinger Job Control utility which processes the two options: The WAIT option forces the glide command to wait until all tasks of the command are completed. This is necessary for the batch jobs to run effectively. The HOST option specifies how tasks are distributed over processors. In addition, the glide option NJOBS distributes the job into subjobs which can number more than the licenses or processors specified in the batch directives.