Rescoring with DOCK 3.7

We often want to get the score for a molecule without doing any docking.

DOCK3.7 now can do this internally. In DOCK 3.6 this was done in an exteranl program scoreopt.

need files

To rescore you need 3 files:

   poses.mol2.gz
   amsol.txt.gz
   vdw.txt.gz

how to generate need files

  run.rescore_prep.csh

Here is a script that will generate the amsol and vdw files from a mol2 file:

  0008.rescore_get_parms_rerun_mod.csh

It will generate the amsol file by reruning amsol using the docked poses.

It is also possible to get the amsol parameters from the db2 files:

  /mnt/nfs/work/tbalius/Water_Project_newgrid_mod_heme_charge/0008.rescore_get_parms_from_db_mod.csh

INDOCK Parameters

Here is the parameters in the INDOCK file:

DOCK 3.7 parameter
#####################################################
### NOTE: split_database_index is reserved to specify a list of files
search_type                   2
mol2file                      poses.mol2.gz
ligsolfile                    amsol.txt.gz
ligvdwfile                    vdw.txt.gz
#####################################################
# NOTE: split_database_index is reserved to specify a list of files
ligand_atom_file               split_database_index

note that the split_database_index file is not used it is just a place holder.