Schrödinger installations at NSC

Directory list:

2013-1 Schrödinger 2013-1

Level of support

Tier 2 NSC has only limited experience with this software, but we will try to help as much as possible. We have ran some tests, for example, if the program comes with a test suite, but they may be far from exhaustive. We will try to install and test new versions, as soon as we can.

Please see the page describing our software support categories for more information.
You can also contact for further information.

The Schrödinger installations are generally maintained by Torben Rasmussen.

Please contact NSC Support if you have any questions or problems.

Official homepage:

The Schrödinger suite includes software for computational chemistry, biomolecular simulations, docking, etc.

You can find more information about the various parts of the Schrödinger suite here:

NSC can provide general help for using the Schrödinger software. We can also provide more in-depth help for using Jaguar, such as help with how to run your Jaguar jobs and to some extend help you with how to set up your Jaguar jobs. We can, for example, help with setting up scripts for running your jobs and help with trouble shooting if you experience issues with running your jobs.

How to run

You can submit jobs from the Maestro GUI, so the easiest way to get started is to start Maestro and then set up and submit your jobs from there.

Most of the Schrödinger products can also be run from the command line. Please contact NSC Support if you need help setting up a script for running jobs with one of the Schrödinger products.

You can find example scripts for running Jaguar under the various Schrödinger distributions.

Starting the Maestro GUI

When running the Maestro GUI (or any of the other variations of the GUI, such as BioLuminate, MaterialsScience, Jaguar, etc.) NSC recommends using ThinLinc to access Triolith.

For more information on how to use ThinLinc, please see:

Starting the GUI

Start a terminal and execute the following on the command line:

$ module load schrodinger/2014-1-nsc
$ maestro

License information

Valid until 2016–05–29.

NSC will strive to continue providing free access to the Schrödinger suite, but availability and job capacity for the various components may change over time. Please provide feedback to NSC Support regarding what components of the suite that are of particular interest for your research.

Please note that our current license only covers reasonably limited use of the Schrödinger suite. Hence, if your research relies heavily on Schrödinger products, we recommend that you obtain your own license for the product(s) that you use most. Your personal license installed at NSC can easily be managed via the NSC Express web portal. That is, you can easily control who will have access to your license by managing a group in NSC Express, adding and removing users to/from this group. You will, of course, also be able to relocate your license by contacting Schrödinger Inc.

Our current license covers the following job capacity:

Product & job type Jobs
COMBIGLIDE, Grid Generation 30
COMBIGLIDE, Library Generation 10
COMBIGLIDE, Protein Prep 30
COMBIGLIDE, Reagent Prep 20
CORE, Hopping Isoteric Matchiung 4
CORE, Hopping Ligand Based 4
GLIDE, Grid Generation 30
GLIDE, Primex Docking 20
GLIDE, Protein Prep 30
GLIDE, SP Docking 15
GLIDE, XP Descriptors 15
GLIDE, XP Docking 15
LIGPREP, Desalter 20
LIGPREP, Ionizer 1000
LIGPREP, Ligparse 20
LIGPREP, Neutralizer 20
LIGPREP, Premin Bmin 20
LIGPREP, Ring Conf 20
LIGPREP, Stereoizer 20
LIGPREP, Tautomerizer 20
MACROMODEL, Autoref 10
MACROMODEL, Confgen 10
MACROMODEL, Csearch Mbae 10
MAESTRO, Unix 1000
PHASE, CL Feature 4
PHASE, CL File Search 20
PHASE, CL Fqsar 4
PHASE, CL Hypocluster 4
PHASE, CL Inactive 20
PHASE, CL Multiqsar 20
PHASE, CL Partition 20
PHASE, CL Phasedb Confsites 20
PHASE, CL Phasedb Convert 20
PHASE, CL Phasedb Manage 20
PHASE, CL Phasedb Search 20
PHASE, CL Qsar 4
PHASE, CL Scoring 20
PHASE, Create Model 4
PHASE, DPM Build Qsar Model 20
PHASE, DPM Common Pharmacaphore 20
PHASE, DPM Create Sites 4
PHASE, DPM Ligprep Clean Structures 20
PHASE, DPM Ligprep Generate Conformers 10
PHASE, DPM Score Hypotheses 20
PHASE, DPM Score Inactives 20
PHASE, FM Find Matches 20
PHASE, MD Add Structures 20
PHASE, MD Create sites 20
PRIME, CM Build Membrane 12
PRIME, CM Build Structure 12
PRIME, CM Edit Alignment 12
PRIME, CM Struct Align 100
PRIME, Threading Search 12