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.

Availability

The Schrodinger suite is available on Oakley and Owens. To view the possibilities, search for schrodinger (macromodel) in the output of module spider   The versions currently available at OSC are:

Version Oakley Owens
2011 X  
2014 X  
2015 X*  
2016   X*
*: Current default version
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 packages:

CANVAS_ELEMENTS
CANVAS_SHARED
MAESTRO_MAIN
MMLIBS
MMOD_CONFGEN
MMOD_MACROMODEL
MMOD_MBAE
GLIDE_SUITE_13OCT2015
CANVAS_MAIN
EPIK_MAIN
FFLD_ACADEMIC
GLIDE_MAIN
GLIDE_XP_DESC
IMPACT_MAIN
KNIME_MAIN
LIGPREP_MAIN
QIKPROP_MAIN
DESMOND_MAIN

Usage

Usage on Oakley

To set up your environment for schrodinger load one of its modulefiles:
module load schrodinger/schrodinger15

 

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=12
#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.

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 -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: