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NEEMP:Getting started

243 bytes added, 13:56, 5 July 2016
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<span style="color'''NEEMP''''s binary and source codes are available online ([http:#FF0000"> waiting for instructions on how //www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.zip'' file containing all the inputs needed to retrieve run the [[NEEMP:Examples | examples]] and get acquainted with the executable file <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/span>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 <code>./neemp</code>. For instance, to get information about basic usage, use:
Click on the link to see the complete [[NEEMP:Options | options list]].
 
Before proceeding in the description of '''NEEMP''''s modes, here we introduce a tree representation of '''NEEMP''''s main directory to assist the user in the examples understanding.
 
'''NB:''' the ''examples'' directory contains all the files employed in the [[NEEMP:examples]] section. ''src'' directory has not been expanded to improve the readability.
<nowiki>
/neemp
├── examples
│ ├── charges.chg
│ ├── ElemBond.par
│ ├── Element.par
│ ├── NOTES
│ ├── set01.sdf
│ ├── set02.sdf
│ └── set03.sdf
├── LICENCE
├── Makefile
├── misc
│ ├── template
│ ├── valgrind-suppresions
│ └── web-update.sh
├── README
└── src
</nowiki>
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