Difference between revisions of "NEEMP:Getting started"

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(Created page with "<span style="color:#FF0000"> waiting for instructions on how to retrieve the executable file </span> '''NEEMP''' can then be run simply by calling the command <code>./neemp</...")
 
 
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<span style="color:#FF0000"> waiting for instructions on how to retrieve the executable file </span>
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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:
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* '''set01.sdf''' -- 500 molecules extracted from DTP NCI with a low atomic element complexity (H, C, N, O, S) 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
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* '''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
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* '''Element.par''' -- parameters calculated using set01 for atomic types determined by element only
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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:
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Click on the link to see the complete [[NEEMP:Options | options list]].
 
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>
 

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.