SERC

SCHRODINGER SOFTWARE SUITE

Introduction

Schrödinger software suite is a drug design software using both ligand and structure-based methods. Schrödinger provides accurate, reliable, and high performance computational technology to solve real-world problems in life science research. It provides superior solutions and services for the design, selection, and optimization of novel drug candidates. Schrödinger's predictive models will enable drug discovery scientists to assess properties of chemical compounds early in the discovery process and to select drug candidates that have optimal profiles.

The predictive power of Schrödinger's software allows scientists to accelerate their research and development activities, reduce research costs, and make novel discoveries that might not be possible with other computational or experimental approaches.

Maestro is a powerful, all-purpose molecular modeling environment. Maestro is the unified interface for all Schrödinger software products.

Vendor : Schrodinger L.L.C., USA.

Supplier : Schrodinger L.L.C., USA

Following software products of Schrödinger are installed at SERC :

  1. First Discovery 2.7
    First discovery 2.7 is a powerful protein modeling suite that consists of
    • Glide
    • Liaison
    • QSite
    • Maestro 6.0
    • Impact
    • Jaguar 5.5
    • MarcModel 8.5
    • Glide
      Glide is designed to assist in high-throughput screening of potential ligands based on binding mode and affinity for a given receptor module.Glide One can compare ligand scores with those of other test ligands or compare ligand geometrics with those of a reference ligand. Additionally one can use Glide to generate one or more plausible binding modes for a newly designed ligand. Once favaourable structures and/or bonding conformations are located with Glide one may use Liaison to obtain binding energies for ligand-receptor pairs.
    • Liaison
      LiaisonLiaison is designed to predict ligand binding energies. Ligands for which binding energies are known are used to calculate the Liaison SVD-fitted parameters-alpha, beta, and gamma. These parameters are subsequently used to predict binding energies for other ligands with the same receptor.
    • QSite
      QSite is mixed mode Quantum MechanicsQSite/Molecular Mechanics program to study geometries and energies of structures not parameterized for use with molecular mechanics, such as those that contain metals or transition states. Qsite is uniquely equipped to perform QM/MM calculations because it combines the superior speed and power of Jaguar.
    • Maestro 6.0
      Maestro 6.0 is the graphical user interaface forMaestro all Schrödinger's products. FirstDiscover (Glide, Impact, Liaison and Qsite) Jaguar, MacroModel etc. It contains tools for building, displaying, and manipulating chemical structures, for organizing, loading and storing these structures and associated data and for setting up, monitoring, and visualizing the results of calculations on these structures.
    • Impact
      Impact is the computational engine that can perform molecular mechanics calculations either through the maestro interface or from the command line.
  2. Jaguar 5.5
    Jaguar 5.5 is designed to increase the Jaguar speed of ab initio calculations in order to accelerate basic and applied research projects and to enable calculations at a higher level of theory. Jaguar's speed and power make it possible to study larger systems than ever before, or to study many more systems than previously possible, within a reasonable time frame.
  3. MarcModel 8.5
    MarcModel, with a large selection of force fields and advanced methods forMarcModel conformational analysis, molecular dynamics, and free energy calculations, is the most trusted name in molecular mechanics. MarcModel is especially well suited for general-purpose molecular mechanics for small and medium-sized organic molecules in both gas and solution phases. Further, MarcModel has powerful utilities for exploring proteins and protein-ligand complexes.

License

Type
:
4/6/8 user, Network / Floating Licenses
Expiry
:
31st December 2017
Manager
:
Flexlm
Server
:
fuel102 (fuel102.serc.iisc.ernet.in)
Modules
:
Available at SERC
Current Usage

Availability

This software is available on all Linux and SGI-Irix machines housed in the computational bays at SERC.

Procedure to use Schrodinger Software Suite

Environmental setup required

SH and KSH - Shells:

  • export PATH=($PATH:/home/pkg/lic/schrodinger)
  • export SCHRODINGER=/home/pkg/lic/schrodinger
  • export LM_LICENSE_FILE=27001@fuel102

CSH and TCSH - Shells:

  • setenv SCHRODINGER /home/pkg/lic/schrodinger
  • setenv LM_LICENSE_FILE 27001@fuel102
  • set path=($path /home/pkg/lic/schrodinger)

How to launch Maestro?

Execute the following command:

maestro

Software documentation:

  1. Each software product has integrated help and tutorials are available as a menu item on the maestro window associated with the software.
  2. Other than the integrated help software associated documentation is available and accessible on any of the access stations in SERC at the following URL:
  3. file:///home/pkg/lic/schrodinger/docs

  4. User can also look for further information at the vendor website at the URL:
  5. http://www.schrodinger.com

  6. The following manuals are available in SERC Library.
    • FisrtDiscovery 2.7 Operating Manual
      (An integrated suite for structure-based drug design)
    • MacroModel 8.5 operating manual
      (The most trusted molecular modeling software)
    • Maestro 6.0 operating manual
      (Graphical user interface for visualization,analysis and project management)
    • Jaguar 5.5 operating manual
      (Extremely fast ab initio electronics structure package )

Report Problems to:

If you encounter any problem in using this software please report to us at the following email address helpdesk@serc.iisc.ernet.in or contact System Administrators in 109 (SERC) for SGI-Irix machines and 109(SERC) for Linux machines.