Rescoring with DOCK 3.7
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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.