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Schrodinger Suite 2012

The graphical front-end for all Schrodinger is called Maestro, and is generally run locally.  Maestro, along with all the other Schrodinger software, can be downloaded here (Linux, Windows, and Mac systems are all supported). The calculations themselves can be run locally, or via the standard bsub command on the Odyssey (check the documentation for each program to see whether parallel calculations are supported).  If calculations are being run locally, it will be necessary to:

 Install the appropriate software from the Schrodinger Download Center (e.g., install Macromodel in addition to Maestro).

 Set an environment variable:

SCHROD_LICENSE_FILE = 27003@rclic1.rc.fas.harvard.edu

The procedure for this depends on your platform and can be found in the documentation from the Schrodinger download center.

 Ensure that you are connected to a Harvard wired network or using a Harvard hosted VPN connected to the RC or FAS vpn realm.

Note: Maestro itself is free, but requires a license. You may either follow the procedure above, or obtain your own license (when you install Maestro, the software will tell you how to do this).

The license system is based on tokens, some of which are interchangeable, and some of which are fixed. We have 25 interchangeable tokens. The use of a program to run one job on one core costs a certain number of tokens for the duration of the job:

- [ 5 ] Glide: ligand-receptor docking (requires 6 tokens when run with XP Descriptors on)

- [ 8 ] Prime: protein structure prediction package

- [ 5 ] Phase: ligand-based pharmacophore modeling

- [ 5 ] CombiGlide for combinatorial library design

- [ 5 ] Core Hopping:  ligand- and receptor-based scaffold exploration

- [ 2 ] QikProp: ADME properties prediction of drug candidates

- [ 4 ] Liaison: binding affinity calculations

- [ 1 ] Epik: pKa calculation in biological conditions

- [ 1 ] SiteMap: identification and characterization of active sites

- [ 1 ] LigPrep: a 2D to 3D conversion program to prepare ligand libraries

- [ 3 ] Jaguar (includes pKa): ab initio quantum mechanics application

- [ 3 ] MacroModel: classical molecular modeling application

- [ 3 ] ConfGen:  bioactive conformational searching

- [ 4 ] QSite: QM/MM application

- [ 1 ] Strike: scientific data analysis program

- [ 2 ] Canvas: customizable cheminformatics platform and interface

- [ 0 ] Maestro: unified graphical interface Workflows

- [ 8 ] Induced Fit Docking (Prime + Glide)

- [ 5 ] QM-Polarized Ligand Docking (Glide + QSite)

- [ 1 ] Protein Preparation Wizard (Epik +Impact (Impact is embedded in Glide))

- [ 8 ] Virtual Screening (Epik, LigPrep, Glide, MacroModel, QikProp, Prime)

Additionally, there are 20 licenses specifically for Macromodel which do not use tokens.  If you are unable to checkout the necessary licensing, your job will not run.  Please write to Research Computing at rchelp@fas.harvard.edu and let us know if you encounter this problem.  Specify the details of the job you are trying to run and the date / time of your attempt.

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