Calculate DOCK6 RMSD: Difference between revisions

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Calculating ligand RMSDs is a tricky thing, but DOCK6 does this quite well.  
Calculating ligand RMSDs is a tricky thing, but DOCK6 does this quite well.  
All you need is two ligands (with the same number of atoms and same Sybil atom types) in mol2 format.
All you need is two ligands in mol2 format (with the same number of atoms and same Sybil atom types) and a DOCK6 binary.


Then you run the following command:
Then you run the following command:
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calc_dock6_rmsd.csh (see code below) outputs three lines:
calc_dock6_rmsd.csh (see code below) outputs three lines:


HA_RMSDs: 4.2878 <br>
HA_RMSDs: 4.2878 <br>
HA_RMSDh: 2.7406 <br>
HA_RMSDh: 2.7406 <br>
HA_RMSDm: 0.9625
HA_RMSDm: 0.9625


The most meaningful line is the one in the middle (HA_RMSDh), which outputs the RMSD using the Hungarian Algorithm (for more information: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm)
The most meaningful line is the one in the middle (HA_RMSDh), which outputs the RMSD using the Hungarian Algorithm (for more information: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm)
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===calc_dock6_rmsd.csh===
===calc_dock6_rmsd.csh===
 
<pre>
  #!/bin/csh -f
  #!/bin/csh -f
  if ($#argv != 2) then
  if ($#argv != 2) then
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         echo "calculates rmsd between 2 molecules using hungarian algorithm implemented in DOCK 6"
         echo "calculates rmsd between 2 molecules using hungarian algorithm implemented in DOCK 6"
     endif
     endif
setenv dock66_dir "/raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook"
   
   
  echo "ligand_atom_file                                            $1" > temp.in
  echo "ligand_atom_file                                            $1" > temp.in
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  echo "score_molecules                                              no" >> temp.in
  echo "score_molecules                                              no" >> temp.in
  echo "atom_model                                                  all" >> temp.in
  echo "atom_model                                                  all" >> temp.in
  echo "vdw_defn_file                                                /raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook/parameters/vdw_AMBER_parm99.defn" >> temp.in
  echo "vdw_defn_file                                                $dock66_dir/parameters/vdw_AMBER_parm99.defn" >> temp.in
  echo "flex_defn_file                                              /raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook/parameters/flex.defn" >> temp.in
  echo "flex_defn_file                                              $dock66_dir/parameters/flex.defn" >> temp.in
  echo "flex_drive_file                                              /raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook/parameters/flex_drive.tbl" >> temp.in
  echo "flex_drive_file                                              $dock66_dir/parameters/flex_drive.tbl" >> temp.in
  echo "ligand_outfile_prefix                                        output" >> temp.in
  echo "ligand_outfile_prefix                                        output" >> temp.in
  echo "write_orientations                                          no" >> temp.in
  echo "write_orientations                                          no" >> temp.in
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  /raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook/bin/dock6 -i temp.in > dock6.log
  $dock66_dir/bin/dock6 -i temp.in > dock6.log
   
   
  grep "HA_RMSD" output_scored.mol2
  grep "HA_RMSD" output_scored.mol2
</pre>
==Acknowledgments==
Thanks to Trent for pointing out this great new feature in DOCK 6.6.
[[Category:Internal]]
[[Category:Docking]]
[[Category:Tutorials]]

Latest revision as of 16:09, 14 February 2014

Calculate ligand RMSDs using DOCK6

Calculating ligand RMSDs is a tricky thing, but DOCK6 does this quite well. All you need is two ligands in mol2 format (with the same number of atoms and same Sybil atom types) and a DOCK6 binary.

Then you run the following command:

~eidamo/work/scripts/calc_dock6_rmsd.csh xtal.mol2 dock.mol2

calc_dock6_rmsd.csh (see code below) outputs three lines:

HA_RMSDs:		4.2878 
HA_RMSDh: 2.7406
HA_RMSDm: 0.9625

The most meaningful line is the one in the middle (HA_RMSDh), which outputs the RMSD using the Hungarian Algorithm (for more information: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm)


calc_dock6_rmsd.csh

 #!/bin/csh -f
 if ($#argv != 2) then
         echo "Usage: $0 mol.mol2 ref.mol2"
         echo "calculates rmsd between 2 molecules using hungarian algorithm implemented in DOCK 6"
     endif
 
 setenv dock66_dir "/raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook"
 
 echo "ligand_atom_file                                             $1" > temp.in
 echo "limit_max_ligands                                            no" >> temp.in
 echo "skip_molecule                                                no" >> temp.in
 echo "read_mol_solvation                                           no" >> temp.in
 echo "calculate_rmsd                                               yes" >> temp.in
 echo "use_rmsd_reference_mol                                       yes" >> temp.in
 echo "rmsd_reference_filename                                      $2" >> temp.in
 echo "use_database_filter                                          no" >> temp.in
 echo "orient_ligand                                                no" >> temp.in
 echo "use_internal_energy                                          no" >> temp.in
 echo "flexible_ligand                                              no" >> temp.in
 echo "bump_filter                                                  no" >> temp.in
 echo "score_molecules                                              no" >> temp.in
 echo "atom_model                                                   all" >> temp.in
 echo "vdw_defn_file                                                $dock66_dir/parameters/vdw_AMBER_parm99.defn" >> temp.in
 echo "flex_defn_file                                               $dock66_dir/parameters/flex.defn" >> temp.in
 echo "flex_drive_file                                              $dock66_dir/parameters/flex_drive.tbl" >> temp.in
 echo "ligand_outfile_prefix                                        output" >> temp.in
 echo "write_orientations                                           no" >> temp.in
 echo "num_scored_conformers                                        1" >> temp.in
 echo "rank_ligands                                                 no" >> temp.in
 
 
 $dock66_dir/bin/dock6 -i temp.in > dock6.log
 
 grep "HA_RMSD" output_scored.mol2

Acknowledgments

Thanks to Trent for pointing out this great new feature in DOCK 6.6.