Difference between revisions of "NEEMP:Getting started"

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'''NEEMP''''s binary file is available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.tar.bz2'' file containing all the inputs needed to run the [[NEEMP:Examples | examples]] and get acquainted with the tool. These files include:
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'''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 V2000
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* '''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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* '''set02.chg''' -- Reference QM charges for all molecules in set02. Theory level, basis set and population analysis: B3LYP/6-311G/NPA
 
* '''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 set03 for atom types determined by element only
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* '''Element.par''' -- parameters calculated using set01 for atomic types determined by element only
  
* '''ElemBond.par''' -- parameters calculated using set03 for atom types determined by element + maximum bond order
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* '''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.