corina usage

Corina is used from the command line. General synopsis is

corina [ -option(s) [suboption[=value],... ] ] [infile [outfile]]

The most important options are -i (input), -o (output) and -d (driver).

Input (-i) suboptions:

• t=sdf, which sets the input file type to sdf 

• sdfi2n=NAME, which copies the data item NAME to the compound name field. The value NAME needs to be changed to coincide that in the sdf-file.
  

Output (-o) suboptions:

• t=mol2, which seta the output file type to mol2 (sdf,rdf,mol,mol2,pdb,ctx, dic, top, par)
  

• nodummies, which suppresses writing of unknown (dummy) atom types in Sybyl mol/mol2 output files.
  

Driver (-d) suboptions:

• wh, write the added hydrogen atoms to the output file.
• rc, multiple ring conformations are generated. The conformations are written in the order of increasing steric energy.
• rs, remove all but the largest fragments for multi-component records (e.g., salts)
• flapn, flap ring nitrogens to generate multiple ring conformations.
• de=value, only conformations having an energy not higher than this value (kJ/mol) with respect to the lowest energy conformation are written to  the output file

All different options and suboptions are explained in the corina manual .