Difference between revisions of "Flex drive.tbl"

From DISI
Jump to navigation Jump to search
m (2 revisions)
Line 39: Line 39:
 
* chem_match_tbl [chem_match.tbl] (string):
 
* chem_match_tbl [chem_match.tbl] (string):
 
# File containing rules for chemical matching
 
# File containing rules for chemical matching
 +
 +
 +
[[Category:Docking]]
 +
[[Category:Tutorials]]
 +
[[Category:jji does not understand]]

Revision as of 03:40, 14 February 2014

This file contains torsion positions assigned to each rotatable bond when the flexible docking parameter is used in DOCK. The drive_id field corresponds to each torsion type in the flex.defn file. The positions field specifies the number of torsion angles to sample. The torsions field specifies the angles that are sampled.

Sample Entries

                   ______________________________________
                   drive_id 2
                   positions 2
                   torsions 0 180
                   ______________________________________
                   drive_id 3
                   positions 3
                   torsions -60 60 180
                   ______________________________________
                   drive_id 4
                   positions 4
                   torsions -90 0 90 180
                   ______________________________________

RETURN TO TABLE OF CONTENTS

NOTE: The following parameter definitions will use the format below:

       parameter_name [default] (value):
       #description

In some cases, parameters are only needed (questions will only be asked) if the parameter above is enforced. These parameters are indicated below by additional indentation.

Atom Typing Parameters

  • atom_model [all] (all, united):
  1. Choice of all atom or united atom models
  • vdw_defn_file [vdw.defn] (string):
  1. File containing VDW parameters for atom types
  • flex_defn_file [flex.defn] (string):
  1. File containing conformational search parameters
  • chem_defn_file [chem.defn] (string):
  1. File containing chemical label definitions
  • chem_match_tbl [chem_match.tbl] (string):
  1. File containing rules for chemical matching