Schrodinger

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.

Important Note: From March 14, 2018, Schrodinger is available from Owens. If you have any questions, please contact OSC Help.

Availability and Restrictions

Versions

The Schrodinger suite is available on Oakley and Owens. The versions currently available at OSC are:

Version Owens
15 X
16  X*
* Current default version

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.

maestro, macromodel, glide, ligprep, qikprep, epik

You can add -l software=glide+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 down below.

Usage

Usage on Owens

To set up your environment for schrodinger load one of its modulefiles:

​​module load schrodinger/schrodinger16

Using schrodinger interactively requires an X11 connection. Typically one will launch the graphical user interface:

maestro 

Here is an example batch script that uses schrodinger non-interactively via the batch system:

# Example glide single node batch script.
#PBS -N glidebatch
#PBS -j oe
#PBS -m ae
#PBS -M srb@osc.edu
#PBS -l walltime=0:10:00
#PBS -l nodes=1:ppn=28
#PBS -l software=glide+1
#PBS -S /bin/sh
qstat -f $PBS_JOBID
export
module load schrodinger
cd $PBS_O_WORKDIR
pbsdcp -p '*' $TMPDIR
cd $TMPDIR
host=`cat $PBS_NODEFILE|head -1`
nproc=`cat $PBS_NODEFILE|wc -l`
glide -WAIT -HOST ${host}:${nproc} receptor_glide.in
ls -l
pbsdcp -p '*' $PBS_O_WORKDIR

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 PBS batch jobs to run effectively. The HOST option specifies how tasks are distributed over processors.

Further Reading

Supercomputer: 
Service: