NEEMP:Getting started

NEEMP's binary file is available online (http://ncbr.muni.cz/NEEMP) together with the examples.tar.bz2 file containing all the inputs needed to run the examples and get acquainted with the tool. These files include:

• set01.sdf -- 500 molecules extracted from DTP NCI with a low atomic element complexity (H, C, N, O, S) and encoded in MOL V2000

• set02.sdf -- 4443 molecules extracted from LigandExpo (ideal coordinates) with high atomic element complexity (H, C, N, O, S, F, Cl, P, Br) and encoded in MOL V3000

• set01.chg -- Reference QM charges for all molecules in set01. Theory level, basis set and population analysis: HF/6-31GH/Mulliken

• set02.chg -- Reference QM charges for all molecules in set02. Theory level, basis set and population analysis: B3LYP/6-311G/NPA

• Element.par -- parameters calculated using set01 for atomic types determined by element only

• ElemBond.par -- parameters calculated using set01 for atomic types determined by element + maximal bond order

NEEMP can then be run simply by calling the command ./neemp. For instance, to get information about basic usage, use:

~/neemp/$ ./neemp --help

Click on the link to see the complete options list.