MOE

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';