SCIENTIFIC APPLICATION – SCHRODINGER

Table of Contents

Overview

Setting up Environment and Invoking from a Research Computing Server

Installing Locally

Notes

Links

Additional Help

Overview

Schrodinger is a suite of molecular modeling packages that take advantage of the latest technological advances in computational chemistry. Jaguar, the high-performance ab-initio quantum mechanics application, and MacroModel, the most trusted name in molecular modeling, have been widely applied to address the full range of chemical research from materials to life sciences. Strike is a chemically aware statistical package for examining structure-property relationships. QSite is a powerful QM/MM application for studying reaction mechanisms in a variety of systems, such as protein active sites.

Also, Schrodinger provides a complete suite of software that addresses the challenges in pharmaceutical research. For structure-based drug design, Prime is an accurate protein structure prediction package; Glide performs accurate, rapid ligand-receptor docking; and Liaison predicts binding affinity. Schrodinger also provides Phase for ligand-based pharmacophore modeling, and QikProp for ADME properties prediction of drug candidates. In addition, LigPrep is a rapid 2D to 3D conversion program that can prepare ligand libraries for further computational analyses. And most recently, Schrodinger introduced CombiGlide for focused library design, and Epik for accurate enumeration of ligand protonation states in biological conditions. Finally, Maestro is the graphical user interface for all of Schrodinger’s computational programs and provides a powerful, fully-integrated molecular visualization and analysis environment.

Research Computing Server(s):	Longleaf
Default Version(s):	2025-2
Installed Version(s):	2025-2

Setting up Environment and Invoking from a Research Computing Server

Maestro, the graphical user interface for all Schrodinger packages, can be accessed through the Research Computing server Longleaf. On Longleaf simply add the package to your environment:

module load schrodinger

module save

Note: If this is your first time using Schrodinger on a Research Computing cluster you will need to create a .schrodinger/tmp directory in your personal /work space. To do this, log into a Research Computing cluster and then do the following two commands:

cd /work/users/<o>/<n>/<onyen>

mkdir –p .schrodinger/tmp

Installing Locally

You can also install Schrodinger locally in your computer. Research Computing provides the installation binary:

• The binary for Schrodinger can be copied from Longleaf to your Windows/LINUX/MacOSX machine from:

/nas/longleaf/rhel9/apps/schrodinger/2025-2/dist/  (or whichever version you want)

• Copy the following files based on your operating system:
  • Users running 64-bit Windows should copy the file: Schrodinger\_Suites\_2025-2\_Windows-x64.zip
  • Users running LINUX OS should copy the file: Schrodinger\_Suites\_2025-2\_Linux-x86\_64.tar
  • Users running MacOSX should copy the file: Schrodinger\_Suites\_2025-2\_MacOSX.dmg
• Once the zip/tar file is downloaded, unpack the file to get installation executable.
• Run the installation program in the unpacked directory to start installation.
• The license file can be downloaded from:

/nas/longleaf/rhel9/apps/schrodinger/2025-2/client_license

• This license also works for PyMOL.
• More information regarding installation of Schrodinger can be found in the README document in the unpacked installation directory.

Notes

• Supported desktop for running Schrodinger is limited to Linux 2.6 only.

• We recently have had subtantial changes in EULA (End User License Agreement). If you are interested in knowing more about it, contact research@unc.edu.

• The following four subsections are relevant to all users, so we paste them here:

  "3.3(a). RESTRICTIONS ON AI/ML: If any machine learning (“ML”) models or ML predictions are trained to, on, using, or based on any data of Schrödinger or generated from the Software (such as, but not limited to, data, simulations, or methodologies) (collectively, “ML Models”), Licensee (i) shall not directly or indirectly, itself or via its contractors, service providers, customers, or other third parties (including, but not limited to, open source libraries or repositories), disclose, incorporate, combine, or distribute any such ML Models to third parties, or (ii) shall use such ML Models only for Licensee’s internal projects. Violation of this Section 3.3(a) shall give rise to Schrödinger having the right to immediately terminate this Agreement by providing written notice to Licensee, and Licensee’s opportunity to cure pursuant to Section 2.2 shall not apply."

  "3.3(b). RESTRICTIONS ON AI/ML: If any ML Model is disclosed (directly or indirectly) to any such third parties (as stated in Section 3.3(a) by Licensee), (i) Licensee shall, within seven (7) days of such disclosure, provide Schrödinger with a copy of the predictions contained in such disclosure, and (ii) Licensee shall delete or destroy all copies of any such disclosed ML Model in its possession or control and shall use best efforts to have all disclosed copies (and derivative works thereof) deleted, destroyed, taken down, and/or removed from access."

  "10.1. ACADEMIC RESTRICTIONS. If Licensee is a university, non-profit or other similar institution purchasing a License to the Software under a Non-Commercial License (as set forth in the Price Quotation), the License granted by Schrödinger is subject to the following usage limitations: (i) only a Qualified Non-Commercial User may use the Software; (ii) the Software may only be used for academic or research purposes and cannot be used, directly or indirectly, for any project that supports, or is supported by, commercial efforts or a commercial enterprise, provided that this restriction shall not apply to basic research projects supported by a commercial enterprise where such commercial enterprise has no commercial or proprietary interest or rights in the outcome of such basic research; and (iii) any results, inventions, or discoveries generated using the Software are to be publicly disclosed and may not be kept confidential or proprietary, and such results or discoveries should be made available in and dedicated to the public domain without restriction. Licensee shall not use the Software for commercial purposes, or maintain the confidentiality of results or discoveries, unless Licensee pays in advance for an upgrade of its Non-Commercial License to a full commercial license pursuant to the then-current pricing generally offered by Schrödinger to its customers. A “Qualified Non-Commercial User” is a student enrolled at an accredited higher education institution, a faculty or staff member employed by an accredited higher education institution, or an employee of a not-for-profit organization or government agency."

  "10.2. ACADEMIC RESTRICTIONS. If Licensee or its licensee, sponsor, or affiliate (including, but not limited to a separate organization affiliated with Licensee for technology development and/or transfer) has a patent application filed (regardless of ownership or who files) which includes at least one claim to a composition of matter, article, method, process, or product-by-process, any of the foregoing of which is based on or contains data obtained from or generated by the Software, Licensee shall immediately after becoming aware of such filing notify Schrödinger in writing thereof. And, in the event of such filing Licensee agrees to pay Schrödinger within thirty (30) days thereof three times the difference between Schrödinger’s then-current standard fee for a Commercial License and Non-Commercial License."

Links

• Official Web site of Schrodinger.

Additional Help

Research Computing home page