Prime User Manual - ISP

1.3 Running Schrödinger Software
Chapter 1: Introduction
To run any Schrödinger program on a UNIX platform, or start a Schrödinger job on a remote
host from a UNIX platform, you must first set the SCHRODINGER environment variable to the
installation directory for your Schrödinger software. To set this variable, enter the following
command at a shell prompt:
csh/tcsh: setenv SCHRODINGER installation-directory
bash/ksh: export SCHRODINGER=installation-directory
Once you have set the SCHRODINGER environment variable, you can start Maestro with the
following command:
$SCHRODINGER/maestro &
It is usually a good idea to change to the desired working directory before starting Maestro.
This directory then becomes Maestro’s working directory. For more information on starting
Maestro, including starting Maestro on a Windows platform, see Section 2.1 of the Maestro
User Manual. There is no need to set SCHRODINGER on Windows: it is set automatically.
Prime jobs, with the exception of Fold Recognition, can be launched from a Windows platform
to a remote UNIX host. You can run Prime MM-GBSA jobs locally on a Windows host.
To launch Structure Prediction jobs from Maestro, you must have access to the PDB. If the
PDB database is not installed into $SCHRODINGER, you must set the SCHRODINGER_PDB environment
variable to the path to the PDB installation. For information on how to set environment
variables on Windows, see Appendix A of the Installation Guide.
1.4 Citing Prime in Publications
The use of this product should be acknowledged in publications as:
Prime, version 2.1, Schrödinger, LLC, New York, NY, 2009.
Prime 2.1 User Manual 3