corina

Generates 3D molecular structures from 2D database

Description

Corina generates 3-dimensional molecular models starting from atom type and connectivity information only. Due to performance and speed Corina can be used in converting large datasets.

Version

• Corina 3.2 is available on Hippu
• Corina 3.2 is available on Murska
• Corina 3.2 available through SOMA2 modeling environment (GUI through web browser)

Usage

On Hippu and Murska, load module file

module load corina

This will enable by default the latest version (3.2).

Basic usage

Corina is used from the command line or from a graphical user interface.

General synopsis is

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

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

Example. Following command line is suitable for generating 3D mol2-files (Sybyl) from sdf-file (MDL/ISIS database) for pharmacophore search purposes:

  
corina -i t=sdf,sdfi2n=NAME -o t=mol2,nodummies -d wh,rc,rs,flapn,de=20 
 		original.sdf converted.mol2

If input file contains several molecules (usually does) they are all written to the one output file (converted.mol2). If the output file is written in mol2 format it can be cut up to single molecules using python script schplit:

schplit converted.mol2

New molecules are named according the value in the field selected with sdfi2n option.

Corina with graphical user interface

Type

corina_direct

Additional information

• Corina home page