Rescoring with DOCK 3.7 - Revision history

TBalius at 15:45, 26 September 2018

2018-09-26T15:45:36Z

← Older revision		Revision as of 15:45, 26 September 2018
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	We often want to get the score for a molecule without doing any docking.		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.		''DOCK 3.7'' now can do this internally. In ''DOCK 3.6'' this was done in an exteranl program ''scoreopt'', which is no longer used.

	== ~~need~~ files ==		== needed files ==
	To rescore you need 3 files:		To rescore you need 3 files:
	poses.mol2.gz		poses.mol2.gz
Line 12:		Line 12:
	== how to generate need files ==		== how to generate need files ==

	Currently, the format of the mol2 file is very rigid. It must be in the same format as mol2s produced by DOCK 3.7.		Currently, the format of the mol2 file is very rigid. It must be in the same format as mol2s produced by ''DOCK 3.7''. The script ''convert_anyMol2_to_dockMol2.py'' should convert mol2 files into the right format.

			Here is a tarball with all the scripts you will need for rescoring (this will likely be provided in a future release of the code):

			[http://docking.org/~tbalius/code/for_dock_3.7/rescoring/rescoring.tar.gz rescoring.tar.gz]

			Here is what is in the tarball:

			drwxr-xr-x tbalius/bks 0 2018-09-26 08:28 rescoring/
			-rw-r--r-- tbalius/bks 429 2018-09-26 08:28 rescoring/1.run.rescore_prep.csh
			-rw-r--r-- tbalius/bks 575 2018-09-26 08:28 rescoring/mol2toDOCK37type.py
			-rw-r--r-- tbalius/bks 1757 2018-09-26 08:28 rescoring/2.rescore_get_parms_rerun_mod.csh
			-rw-r--r-- tbalius/bks 1725 2018-09-26 08:24 rescoring/convert_anyMol2_to_dockMol2.py
			-rw-r--r-- tbalius/bks 32030 2018-09-26 08:21 rescoring/mol2.py
			-rw-r--r-- tbalius/bks 3074 2018-09-26 08:19 rescoring/separate_mol2_more10000.py


	The following script will process a mol2 file produced by dock for rescoring.		The following script will process a mol2 file produced by dock for rescoring.

TBalius: /* how to generate need files */

2017-11-29T18:50:41Z

how to generate need files

← Older revision		Revision as of 18:50, 29 November 2017
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	It will generate the amsol file by reruning amsol using the docked poses.		It will generate the amsol file by reruning amsol using the docked poses.

			You could download the amsol file for the promoter of interest from zinc15.
			for example:
			curl http://files.docking.org/protomers/08/06/14/455080614.solv > output.solv2
			process it for dock:
			echo "########$name########" >> amsol.txt
			paste vdw.txt output.solv2 \| awk '{printf"%2s %3s %5s %5s %5s %5s\n", $1, $2, $5, $6, $7, $8}' >> amsol.txt


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

TBalius: /* how to generate need files */

2017-11-29T18:36:53Z

how to generate need files

← Older revision		Revision as of 18:36, 29 November 2017
Line 11:		Line 11:

	== how to generate need files ==		== how to generate need files ==

			Currently, the format of the mol2 file is very rigid. It must be in the same format as mol2s produced by DOCK 3.7.

			The following script will process a mol2 file produced by dock for rescoring.
	1.run.rescore_prep.csh		1.run.rescore_prep.csh

	Here is the script:		Here is the script:

TBalius: /* how to generate need files */

2017-11-29T18:27:04Z

how to generate need files

@@ Line 11: / Line 11: @@
 == 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:
-Here is a script that will generate the amsol and vdw files from a mol2 file:
+.rescore_get_parms_rerun_mod.csh
-.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 ==

TBalius: Created page with " 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. =..."

2016-04-26T23:46:18Z

Created page with " 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. =..."

New page

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.