Schrödinger installations at NSC


Directory list:

VersionDescription
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 support@nsc.liu.se 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: www.schrodinger.com

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: www.schrodinger.com/productsguide

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: www.nsc.liu.se/systems/triolith/#accessing_triolith_thinlinc

Starting the GUI

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

$ module load schrodinger/2013-1-nsc
$ maestro

License information

Valid until 2014–05–29.

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
BIOLUMINATE 10
BIOLUMINATE, Shared 10
CANVAS 100
COMBIGLIDE, Grid Generation 40
COMBIGLIDE, Library Generation 15
COMBIGLIDE, Protein Prep 40
COMBIGLIDE, Reagent Prep 30
COMBIGLIDE, SP Docking 7
CORE, Hopping Isoteric Matchiung 6
CORE, Hopping Ligand Based 6
EPIK 30
GLIDE, Grid Generation 40
GLIDE, Primex Docking 30
GLIDE, Protein Prep 40
GLIDE, SP Docking 10
GLIDE, XP Descriptors 10
GLIDE, XP Docking 10
IMPACT 40
JAGUAR 20
JAGUAR, PKA 20
KNIME 100
LIGPREP, Desalter 30
LIGPREP, Ionizer 1000
LIGPREP, Ligparse 30
LIGPREP, Neutralizer 30
LIGPREP, Premin Bmin 30
LIGPREP, Ring Conf 30
LIGPREP, Stereoizer 30
LIGPREP, Tautomerizer 30
MACROMODEL 15
MACROMODEL, Autoref 15
MACROMODEL, Confgen 15
MACROMODEL, Csearch Mbae 15
MACROMODEL, Minta 15
MAESTRO, Unix 1000
MMLIBS 1000
PHASE, CL Feature 6
PHASE, CL File Search 30
PHASE, CL Hypocluster 6
PHASE, CL Inactive 30
PHASE, CL Multiqsar 30
PHASE, CL Partition 30
PHASE, CL Phasedb Confsites 30
PHASE, CL Phasedb Convert 30
PHASE, CL Phasedb Manage 30
PHASE, CL Phasedb Search 30
PHASE, CL Qsar 6
PHASE, CL Scoring 30
PHASE, Create Model 6
PHASE, DPM Build Qsar Model 30
PHASE, DPM Common Pharmacaphore 30
PHASE, DPM Create Sites 6
PHASE, DPM Ligprep Clean Structures 30
PHASE, DPM Ligprep Generate Conformers 15
PHASE, DPM Score Hypotheses 30
PHASE, DPM Score Inactives 30
PHASE, FM Find Matches 30
PHASE, MD Add Structures 30
PHASE, MD Create sites 30
PRIMEX 3
PRIME, CM Build Membrane 10
PRIME, CM Build Structure 10
PRIME, CM Edit Alignment 10
PRIME, CM Struct Align 80
PRIME, Threading Search 10
QIKPROP 15
QSITE 20
SITEMAP 30
STRIKE 30