Exons:
Relevant bits of information for using the MUSC Shared Resource,
 the BioMolecular Computing Resource (BCR).

Exon_66 Schrodinger Programs at MUSC.

MUSC has licensed four Schrodinger products. These are:

JAGUAR 4.1: Quantum Mechanical Calculations
MACROMODEL 7.1: General Purpose Molecular Modeling including dynamics and minimization.
MAESTRO: 3.0 A common GUI for Macromodel and Jaguar
MOPAC2000 Molecular Orbital Package with high capacity for proteins

Modify your ".cshrc" file to include the following lines.


#Schrodinger MOPAC2000 setup
setenv MOPAC_HOME /usr/common/bcr/mopac
set path = ($path $MOPAC_HOME)
#Schrodinger Maestro/MacroModel/Jaguar setup
setenv SCHRODINGER /usr/common/bcr/macromodel
alias macromodel $SCHRODINGER/macromodel
alias maestro $SCHRODINGER/maestro
alias jaguar $SCHRODINGER/jaguar

To start the master GUI MAESTRO simply add the above to your .cshrc file, 
save the changes, type "source .cshrc" OR logout/login again.
Then type "maestro &". 
The "regular" interface to macromodel may be started by typing "macromodel"
and then selecting an appropriate terminal type.
MAESTRO/MACROMODEL are available from photon,janus and lobo but NOT erg2 or quark!

JAGUAR is available on lobo only. You may simply
type jaguar & or launch MAESTRO and start JAGUAR from the 
MAESTRO interface. JAGUAR has a built-in BABEL program and
can read/convert most formats. MACROMODEL can read PDB and SYBYL
MOL2 formats.

Typing "mopac2000" will launch the program but you must have a
properly formated coordinate file named test.dat. This file is 
most readily created by the standalone 
babel program.
Alternatively, use the MAESTRO/JAGUAR program to create a
suitable formatted file for your MOPAC200 input. 



     
 

The BCR at the Medical University of South Carolina
URL: http://bcr.musc.edu/
Last modified: March 19,2001- ESH

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