Laboratory for Molecular Simulation

Director: Michael B. Hall Manager: Lisa M. Pérez

Phone: (979) 845-9384Fax (979) 845-2971Rm. 2109 Chemistry
e-mail: mouse@mail.chem.tamu.edu

MacroModel

by Schrödinger

The MacroModel program has a large selection of force fields and advanced methods for conformational analysis, molecular dynamics, and free energy calculations, MacroModel is the most trusted name in molecular mechanics and is especially well suited for general-purpose molecular mechanics for small and medium-sized organic molecules in both gas and solution phases.

SCHRÖODINGER Home Page User Manuals Running MacroModel Patches Trouble-Shooting

Running Macromodel:

Maestro is the GUI for MacroModel and also works as an interface for other SCHRÖDINGER software (Jaguar, Glide, Liaison, QikProp, and QSite).

To run Maestro and/or XCluster:

chmsgi and any SGI machine that is running IRIX 6.5 or later and has chmsgi:/chem mounted you will need to add the following line to your .tcshrc file:

setenv SCHRODINGER /chem/mmod71
setenv MMEXECDIR $SCHRODINGER/macromodel-v71008/bin/IRIX-mips4
setenv BATCH_ROOT $SCHRODINGER/macromodel-v71008/data
alias maestro $SCHRODINGER/maestro
alias xcluster $SCHRODINGER/xcluster

k2 - you will need to add the following line to your .tcshrc file:

setenv SCHRODINGER /usr/local/lms/mmod71
setenv MMEXECDIR $SCHRODINGER/macromodel-v71008/bin/IRIX-mips4
setenv BATCH_ROOT $SCHRODINGER/macromodel-v71008/data
alias maestro $SCHRODINGER/maestro
alias xcluster $SCHRODINGER/xcluster

To run Maestro, type: maestro at the prompt

Trouble-Shooting:

If you are running on a remote machine and you receive the error:

Xlib: connection to "labmol4.chem.tamu.edu:0.0" refused by server
Xlib: Client is not authorized to connect to Server
Error: Can't open display:labmol4.chem.tamu.edu:0.0

(where labmol4.chem.tamu.edu will be replaced by the local machine name)

You need to use X11 forwarding to access the remote machine (ssh -X username@remote_machine_name or you may also need to use the -Y flag ssh -X -Y username@remote_machine_name )

error:
maestro: Command not found.

The alias that you created in your .tcshrc is either incorrect or has not been activated yet. Check the line in your .tcshrc file and make sure it matches the commands given above. To activate the modified .tcshrc you may logout and log back in or simply type:

source .tcshrc

This source command will activate any changes made to your .tcshrc file.

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