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MacroModel

Introduction

The MacroModel molecular modeling software package allows the user to construct and graphically manipulate both simple and complex chemical structures, to apply molecular mechanics and dynamics techniques to evaluate the energies and geometries of molecules in vacuo or in solution, and to display and examine graphically the results of the modeling calculations.

Version

Several versions are currently available at OSC. The latest installed version is 9.8.

Availability

MacroModel is available on the BALE Cluster and the Glenn Cluster.

Usage

A batch process is required when running MacroModel, either interactively or non-interactively. For interactive use with an X11 interface, you must be prepared to take part in an X11 session. Additionally, if you will use 3D graphics, your workstation must support the OpenGL X11 extensions. For a quick test of your connection, run the command "glxgears." If successful, animated gears will appear in a window on your terminal.

For more information about client-server protocols and X11, read the OSC FAQ web page, http://www.osc.edu/supercomputing/faq.shtml#sshwindows

As A Module
MacroModel is installed under the module paradigm; therefore you should have the modulefile macromodel loaded before you try to use MacroModel.
module load macromodel

The latest installed version can be accessed via
module load macromodel9.8

Interactive
To interactively use the maestro interface, bring up an interactive batch job. [Here is a sample session] :

userid@opt-login1> qsub -V -I -l walltime=01:00:00 -l nodes=1:ppn=1

[The use of the -V flag declares that all environment variables in the  qsub  command's environment are to be exported to the batch job. This will include the necessary environment settings for the X11 protocols.]
qsub: waiting for job 330978.nfs4.osc.edu:17001 to start
qsub: job 330978.nfs4.osc.edu:17001 ready

tset: unknown terminal type unknown
Terminal type? xterm
Enter UNIX terminal type, Terminal type? [vt100] xterm
[opt0747]% module load macromodel
[opt0747]% maestro

Maestro Molecular Modeling Interface
Copyright 1999-2003 Schr\uffffdinger, L.L.C.
Portions of this program include material copyrighted (c)
by Absoft Corporation 1988-1998
**********************************************************************
Checking environment variables...

SCHRODINGER:  /usr/local/schrodinger
MAESTRO_EXEC: /usr/local/schrodinger/maestro-v60107/bin/Linux-x86
LD_LIBRARY_PATH: /usr/local/schrodinger/maestro-v60107/lib/Linux-x86:
/usr/local/globus-2.4.3/lib:/usr/local/mpich-1.2.6-
ib/lib/shared:/usr/local/infiniband/lib:/usr/local/pvfs2/lib:
/usr/local/globus/lib:/usr/local/pgi-5.1.3/linux86/5.1/lib:/usr/local/mkl-
7.0.17/mkl70/lib/32:/usr/local/intel-8.0-20040716/lib
MMSHARE_EXEC: /usr/local/schrodinger/mmshare-v12014/bin/Linux-x86
MMOD_EXEC: /usr/local/schrodinger/macromodel-v85014/bin/Linux-x86

FIFO_LOCATION Environment Variable Not Defined
Setting and Using Default
FIFO_LOCATION  = /tmp/28729
TEMP_PROJECT Environment Variable Not Defined
Setting TEMP_PROJECT to $TMPDIR/$USER
TEMP_PROJECT  = /tmp/pbstmp.330978/userid
mkdir -p /tmp/pbstmp.330978/userid

Environment variables successfully initialized.  Starting up Maestro...
[After a minute, the maestro interface, the gui for all of Schrodinger's applications, will appear on your display.]

Non-interactive
For non-interactive use, a batch script is needed. [An example batch file follows.]:

my_mm_batch.job:
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=1
#PBS -N my_mm
#PBS -S /bin/ksh
#PBS -j oe

module load macromodel
bmin -WAIT inputfile

The macromodel commands, as well as maestro, pass control to the Schrodinger Job Control utility. The WAIT flag disables returning to the prompt, or scheduler, until the job is completed. This is necessary for PBS batch jobs to run effectively. When running interactively and using the macromodel commands from the command line, the use of WAIT option is recommended. Otherwise, the batch job might be exited, thus killing any processes initiated, before the macormodel processes are completed.

Documentation

PDF formatted documentation may be downloaded using 'scp':

1. $SCHRODINGER/docs/general/*/*.pdf
2. $SCHRODINGER/docs/macromodel/*/*.pdf
3. $SCHRODINGER/docs/maestro/*/*.pdf