Schrödinger Suite 2011 Windows Release Notes

These release notes are for the Schrödinger Suite 2011 Update 1 software released in September 2011.

Software Requirements

Schrödinger software is supported on the following operating systems:

The following software is also required:


The Windows version of Maestro generally supports all the structure and project management features that are in the UNIX version. A few features that have UNIX dependencies were removed.

The preparation and launching of local jobs (i.e. on the Windows computer where Maestro is installed) from Maestro is supported for all products and workflows, with the following exceptions:

The preparation and launching of remote jobs from Maestro to UNIX hosts is supported for all products, with the following exceptions:

You can display the panels for some products listed above, but you cannot run jobs for these products from Maestro.

Installing Schrödinger Software

Instructions for installing and uninstalling are given in the Installation Guide. This document is available in PDF format along with the README and the Release Notes on the DVD or in the download zip file. Note that, since Maestro no longer uses an X server, any references to an X server in the Installation Guide can be ignored.

Once you have installed the software, you must also install a license — see the Licenses section for instructions.

Schrödinger software includes .ini files that are not Windows .ini files. If you are using product management software (such as Zenworks), you will have to ensure that these files are treated as plain files and not as Windows .ini files.

To submit jobs to UNIX hosts from the Windows version of Maestro, you must install the corresponding products on the remote UNIX hosts, and you must install the product or the client for the product on the local Windows host. This is because launching a job requires a local installation. You must also ensure that the schrodinger.hosts file on the Windows host includes settings that point to the UNIX installations.

You can download the UNIX software from our web site, If you would prefer a DVD, please contact Schrödinger.

To import PDB files from a local copy of the PDB and to launch Prime Structure Prediction jobs using this copy, you must set the environment variable SCHRODINGER_PDB to the full path to an installation of the PDB.

Note: Shared user resources are stored in %APPDATA%\Schrodinger, so that they can be shared across machines. These resources include Maestro preference files such as prefer.cmd and maestro.cmd, and scripts downloaded from the web. Local resource files, such as the job database, temporary projects, customized hosts and license files, are stored in %LOCALAPPDATA%\Schrodinger

Uninstalling Schrödinger Software

You must use setup.exe to uninstall the software, either directly or indirectly as explained below. Use of Add/Remove Programs to uninstall the software has been disabled because it does not perform all the necessary actions to completely remove the installation.

For releases earlier than Suite 2009 Update 2, you must use the original setup.exe. From Suite 2009 Update 2 on, you can also uninstall the software using uninstall.exe, which is a limited copy of setup.exe in the installer folder of your Schrödinger software installation (%SCHRODINGER%\installer). You can run this uninstaller by going to Start > Programs > Schrodinger-year > Uninstall.

If you have installed the Schrödinger KNIME Extensions, you must remove them manually from the installation, by removing the folder knime-vversion and the script file knime.bat. The installer does not remove them.


To run Maestro you must have a Maestro Windows license. If you are an academic user, the license is provided with the software and is automatically installed in the top level of your Schrödinger software installation. Otherwise, you must obtain a license from Schrödinger.

To obtain a license, you should send the required information to The information that you need is displayed in a dialog box that opens when you try to run Maestro without a license. You can copy and paste the text from this dialog box into an email message, or you can attach the file described in the dialog box text to an email message. The file is named schrodinger_machinfo.txt, and is written to your desktop.

Schrödinger will send you a license code, which you will need to insert into the license file, named license.txt. You can use Wordpad or a similar program to enter the license code information into this file. If you have a node-locked license, this file is stored in the installation directory on the local host (your Windows machine). If you have a token-based license, this file is stored in the installation directory of your license server.

If you have a token-based license, there are two ways in which you can enable access to the license server:

To run Schrödinger products, you must have the necessary licenses for that product.


Documentation for all products has been included and is installed automatically. The documentation is available from the Maestro Help menu and in the docs folder of your installation.

To display the documentation, you must have a browser and a PDF viewer installed. The defaults are Internet Explorer and Adobe Reader. Note that Adobe Reader 8.0 is not supported: you should upgrade to a more recent version (at least 8.1).

Running Maestro

You can run Maestro either by double-clicking the desktop icon or selecting Maestro from the Schrodinger submenu of the Program menu.

Launching Remote Jobs from Maestro

To launch a remote job from Maestro you must do the following:

You can launch remote jobs from Maestro or from the command line. To launch jobs from the command line, you can open a Schrödinger shell (from the Start menu), and use Unix commands for starting a job. The Schrödinger shell is a limited implementation of a Unix shell and does not support all the commands of a native Linux implementation, such as bash or csh.

Note: When you submit a remote job from Maestro, you must choose the appropriate remote host from the Host menu in the Start dialog box.

Setting Environment Variables

Environment variables are set in the Environment Variable dialog box, which you open as follows:

Windows XP:

  1. Right-click on My Computer, and choose Properties from the shortcut menu.

    The System Properties dialog box opens.

  2. In the Advanced tab, click Environment Variables.

    The Environment Variables dialog box opens.

Windows Vista:

  1. Click Start, then click Control Panel from the shortcut menu.

    The Control Panel opens.

  2. Click User Accounts.

  3. Click User Accounts again.

  4. In the Task list in the side pane, click Change my environment variables.

    The Environment Variables dialog box opens.

To set a new environment variable:

  1. In the User variables section, click New.

    The New User Variable dialog box opens.

  2. Enter the name of the variable and its value, and click OK

    The New User Variable dialog box closes.

To modify an existing environment variable:

  1. Right-click on My Computer, and choose Properties from the shortcut menu.

    The System Properties dialog box opens.

  2. In the Advanced tab, click Environment Variables.

    The Environment Variables dialog box opens.

  3. In the User variables section, select the environment variable that you want to change.

  4. Click Edit.

    The Edit User Variable dialog box opens.

  5. Change the value of the variable and click OK.

When you have finished setting environment variables, click OK in the Environment Variables dialog box to save the values. You can then close the System Properties dialog box (XP) or Control Panel (Vista).

Reporting Problems

If you have problems with the installation, please send the following files, which are in the directory %LOCALAPPDATA%\Schrodinger\2011, to

You should also send the file schrodinger_machid.txt, which is on your desktop. If you have installed versions for more than one release, there will be multiple copies of this file, named schrodinger_machid-N.txt, where N is a number. In this case you should check that you send the correct version of the file (which will usually be the latest version).

If Maestro does not start, send email to describing the circumstances, and attach the file maestro_error.txt from the directory %LOCALAPPDATA%\Schrodinger\appcrash\ to your email message. If Maestro fails after startup, attach this file and the file maestro.EXE.dmp (from the same directory) to your email message. These files will help us to diagnose the problem.

%LOCALAPPDATA% is set to C:\Users\username\AppData\Local on Windows Vista and Windows 7 (and related server platforms). On Windows XP, it is not set by default. The appropriate path is C:\Documents and Settings\username\Local Settings\Application Data.

If you encounter the following error, we request that you download RegDllView from, run it and send us the output.

Error 1720. There is a problem with this Windows Installer package. A script required for this install to complete could not be run. Contact your support personnel or package vendor.

When sending e-mail messages, please include the following information:

Much of this information is in the file schrodinger_machid.txt, which is on your desktop.

Known Issues

For this release, the following issues should be noted:

Known issues for Maestro in general can be found at the Support Center. Each product has a separate Known Issues page, which includes issues about the Maestro interface for the product as well as the executables.