Difference between revisions of "NEEMP:Getting started"
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| − | '''NEEMP''''s binary | + | '''NEEMP''''s binary and source codes are available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.zip'' file containing all the inputs needed to run the [[NEEMP:Examples | 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 | * '''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 | + | * '''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 | * '''set01.chg''' -- Reference QM charges for all molecules in set01. Theory level, basis set and population analysis: HF/6-31GH/Mulliken | ||
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* '''Element.par''' -- parameters calculated using set01 for atomic types determined by element only | * '''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 + | + | * '''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: | '''NEEMP''' can then be run simply by calling the command <code>./neemp</code>. For instance, to get information about basic usage, use: | ||
Latest revision as of 16:56, 5 July 2016
NEEMP's binary and source codes are available online (http://ncbr.muni.cz/NEEMP) together with the examples.zip 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.