Difference between revisions of "MOE"
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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 []; " | ||
| + | ##################################################### | ||
| + | |||
| + | The exact formatting presented above is important, otherwise the script will not work. Note the positioning of \ and ; exactly. If you have moe installed and for additional commands see "MOE Function Index" located at "file:///c:/moe/html/fcnindex.html". | ||
| + | |||
| + | SVL scripts can be run as | ||
| + | moebatch -script charge.svl | ||
| + | |||
| + | For SVL scripts, specifying a function is necesary, otherwise MOEbatch will fail (stating that it could not | ||
| + | find the function even though it was loaded). | ||
| + | // function FUNCTION_NAME; | ||
| + | function charge_acs_receptor; | ||
| + | ReadTriposMOL2 'rec_min.mol2'; | ||
| + | WriteTriposMOL2 'rec.amber99.mol2'; | ||
Latest revision as of 15:59, 15 July 2011
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 []; " #####################################################
The exact formatting presented above is important, otherwise the script will not work. Note the positioning of \ and ; exactly. If you have moe installed and for additional commands see "MOE Function Index" located at "file:///c:/moe/html/fcnindex.html".
SVL scripts can be run as
moebatch -script charge.svl
For SVL scripts, specifying a function is necesary, otherwise MOEbatch will fail (stating that it could not find the function even though it was loaded).
// function FUNCTION_NAME; function charge_acs_receptor; ReadTriposMOL2 'rec_min.mol2'; WriteTriposMOL2 'rec.amber99.mol2';
