SCHRÖDINGER is an extensive suite of applications for molecular modelling, molecular mechanics and quantum chemistry used to solve real-world problems in life science research such as drug discovery and materials design. The graphical interface called Maestro can be used to build, edit and analyse molecules interactively and to submit jobs. For more details, please consult the SCHRÖDINGER Home page.


SCHRÖDINGER Applications

ApplicationBinary NamePurpose
AutoQSARautoqsarCreation and application of predictive QSAR models
BioLuminatebioluminateModeling solution for biologics
CanvascanvasCheminformatics computing environment
ConfGenconfgenBioactive conformational searching
Ligand- and receptor-based scaffold exploration for lead optimization
CovDockcovalent_dockingPose prediction and scoring of covalently bound ligands
DesmonddesmondMolecular dynamics simulations
EpikepikpKa predictions
Field-Based QSARphase_fqsarLead discovery/optimization using quantitative predictions of binding-site chemistry
GlideglideLigand-receptor docking
Induced FitifdPrediction of ligand induced conformational changes in receptor active sites
Jaguarjaguarab initio electronic structure package
KNIME ExtensionsknimeFramework for easy workflow automation and data analysis
LigPrepligprepGeneration of 3D molecular ligand models
MacroModelmacromodelMolecular modeling
MaestromaestroMolecular modeling environment
Phasephase_XXXPharmacophore modeling for ligand- and structure-based drug design
PrimeprimeProtein structure predictions
PrimeXprimexProtein crystal structure refinement
Protein Preparation WizardprepwizardCorrecting common structural problems and creating reliable, all-atom protein models
QM-Polarized Ligand DockingqpldDocking using a combinination of Glide and QSite
QikPropqikpropADME predictions of drug candidates
QSiteqsiteQM/MM program
Shape Screeningshape_screenVirtual screening with 3D shape-based similarity
SiteMapsitemapBinding site identification

Please note that the number of licenses/tokens for SCHRÖDINGER applications is limited to 50 floating licenses at LRZ. Furthermore, each user can utilize up to a maximum of 15 licenses/tokens at the same time.


The environment modules package controls access to the software. Use "module avail schrodinger" to find all available versions of SCHRÖDINGER installed at LRZ.

To use the default version of SCHRÖDINGER, please type:

> module load schrodinger

Running SCHRÖDINGER applications via Maestro

You can either start Maestro on the login nodes of Linux-Cluster & SuperMUC-NG or by using our remote visualization service (via VNC). We however want to note that the graphics performance on the login nodes is comparatively poor. Therefore, we recommend our users to only start Maestro on the login nodes for less demanding visualisations of e.g. small molecules. Please submit (via "Job Settings", "Host List") jobs of SCHRÖDINGER applications (see list above) to seperate hosts such as mpp2 but not to the "localhost" resources of the login nodes. In the case of using our remote visualization service (via VNC) to visualize larger data sets, you will however entirely have access to the reserved "localhost" node including GPU resources and can therein submit jobs of SCHRÖDINGER applications within Maestro.

To start Maestro graphical user interface, simply type:

> maestro

Alternatively, you can start Maestro using profiles. To launch Maestro Elements, Bioluminate or Materials Science GUI, simply type one of the following commands:

> maestro -profile Elements
> maestro -profile BioLuminate
> maestro -profile MaterialsScience

Running SCHRÖDINGER applications via the command line

Alternatively, you can run all SCHRÖDINGER applications via the command line, i.e., without Maestro. This way of usage is especially recommended in view of high throughput.

Via an interactive SLURM shell (recommended for a few jobs or testing purposes)

To e.g. request one node on cm2 of the Linux Cluster for half an hour, please issue:

> salloc --nodes=1 --time=00:30:00 --partition=cm2_inter

For requesting one node on the test partition of SuperMuc-NG for half an hour, please issue:

> salloc --nodes=1 --time=00:30:00 --partition=test --account <project id>

When a new batch session is returned to you, simply type


to run your SCHRÖDINGER application (for BINARY_NAME, please see the table above).

By submitting a SLURM batch script (recommended for production runs)

For production runs, please create a SLURM batch script and submit via "sbatch".

Linux Cluster


#SBATCH -o /dss/dsshome1/<group>/<user>/mydir/%x.%j.out
#SBATCH -e /dss/dsshome1/<group>/<user>/mydir/%x.%j.err #SBATCH -D /dss/dsshome1/<group>/<user>/mydir #SBATCH -J <job_name>
#SBATCH --time=24:00:00
#SBATCH --clusters=cm2_tiny
#SBATCH --nodes=1 #SBATCH --export=NONE #SBATCH --get-user-env #SBATCH --mail-type=end #SBATCH --mail-user=<email_address>@<domain> module load slurm_setup
module load schrodinger
#SBATCH -o /dss/dsshome1/<group>/<user>/mydir/%x.%j.out
#SBATCH -e /dss/dsshome1/<group>/<user>/mydir/%x.%j.err
#SBATCH -D /dss/dsshome1/<group>/<user>/mydir
#SBATCH -J <job name>
#SBATCH --time=24:00:00
#SBATCH --partition=micro
#SBATCH --nodes=1
#SBATCH --export=NONE
#SBATCH --get-user-env
#SBATCH --mail-type=END
#SBATCH --mail-user=<email_address>@<domain>
#SBATCH --account=<project id>

module load slurm_setup
module load schrodinger



The SCHRÖDINGER installation provides manuals in html and pdf format. They are accessible from the Maestro interface page at "help" or via the environment variable $SCHRODINGER_DOCFor further information, please refer to the SCHRÖDINGER Home page.


If you have any questions or problems with SCHRÖDINGER installed on different LRZ platforms, please don't hesitate to contact LRZ HPC support staff.

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