Difference between revisions of "MOE"
From Rizzo_Lab
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A nice tutorial written by Thomas W. Shattuck in the Department of Chemistry at Colby College is [http://www.colby.edu/chemistry/CompChem/MOEtutor.pdf here]. | A nice tutorial written by Thomas W. Shattuck in the Department of Chemistry at Colby College is [http://www.colby.edu/chemistry/CompChem/MOEtutor.pdf here]. | ||
| + | |||
| + | ==SVL Programming== | ||
| + | SVL programming is best written as a tcsh script calling moebatch command-line as shown below. MM functions minimizes the molecule. pot_load assigns a forcefield. | ||
| + | ##################################################### | ||
| + | /opt/moe/bin/moebatch -exec "\ | ||
| + | ReadTriposMOL2 '121P.lig.am1bcc.mol2'; \ | ||
| + | pot_Load '/opt/moe/lib/mmff94x.ff' | ||
| + | MM [ pot_charge:0, keep_chirality:'geometry' ]; | ||
| + | WritePDB 'temp.pdb'; \ | ||
| + | WriteMOE 'temp.moe'; \ | ||
| + | WriteTriposMOL2 'temp.mol2'; \ | ||
| + | Close []; " | ||
| + | ##################################################### | ||
Revision as of 18:30, 27 July 2010
MOE stands for Molecular Operating Environment. Apart from being a great visualization software, it can also used as a molecule builder and doing energy minimization.
A nice tutorial written by Thomas W. Shattuck in the Department of Chemistry at Colby College is here.
SVL Programming
SVL programming is best written as a tcsh script calling moebatch command-line as shown below. MM functions minimizes the molecule. pot_load assigns a forcefield.
##################################################### /opt/moe/bin/moebatch -exec "\ ReadTriposMOL2 '121P.lig.am1bcc.mol2'; \ pot_Load '/opt/moe/lib/mmff94x.ff' MM [ pot_charge:0, keep_chirality:'geometry' ]; WritePDB 'temp.pdb'; \ WriteMOE 'temp.moe'; \ WriteTriposMOL2 'temp.mol2'; \ Close []; " #####################################################
