Editing NEEMP:Modes (section)

=Calculation mode=

'''''<u>BASIC USAGE:</u>''''' ''./neemp -m charges --sdf-file examples/set01.sdf --par-file examples/ElemBond.par --chg-out-file eem_charges''

To compute EEM charges with '''NEEMP''', it is necessary to provide the SDF file with molecules for which the charges will be computed (option <code>--sdf-file</code>) and the PAR file with EEM parameters (option <code>--par-file</code>). EEM charges will be written into the file specified by <code>--chg-out-file</code> option.

The user should keep in mind that, because of the EEM method itself, the EEM charges cannot be computed for atoms or atomic types for which the parameters are missing. This situation is well depicted by '''''Figure 1'''''. On the left side the parameter set contains values for all the atomic types in ''set01.sdf'', on the other hand in the right side image it is evident how the same parameter set is lacking values for several atomic types present in ''set02.sdf'', leading to the discard of many molecules (for details on the syntax, see the [[NEEMP:Examples#Example 2 - Calculation mode | examples]] or [[NEEMP:Options | option list]] section).
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto;" width="650px"
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 | [[File:chg_new1.png| 450px]]
 | [[File:chg_new2.png| 450px]]
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 |colspan=2 |'''''Figure 1:''''' The lack of parameter values in the parameter set file ''ElemBond.par'' for the atomic types highlighted in the right side image causes the discarding of several molecules from ''set02.sdf'', emphasized by the drop in the covered molecules percentage.
 |}