DOCK3.7 INDOCK Minimization Parameter - Revision history

TBalius: /* Information on number_save and number_write parameters */

2017-11-15T00:19:10Z

Information on number_save and number_write parameters

← Older revision		Revision as of 00:19, 15 November 2017
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	This is true for DOCK v3.7.1rc1 (and later versions).		This is true for DOCK v3.7.1rc1 (and later versions).

	"number_save" is the number that are minimized and written to OUTDOCK.		"number_save" is the number (for each hierarchy) that are minimized and written to OUTDOCK.

	"number_write" are the number that are written to the mol2 file.		"number_write" are the number (for each hierarchy) that are written to the mol2 file.

	For example, if you set number_save to 10 and number_write to 2 then 10 poses will be minimized but only the top two scoring minimized poses will be written out to the mol2 file.		For example, if you set number_save to 10 and number_write to 2 then 10 poses will be minimized but only the top two scoring minimized poses will be written out to the mol2 file.

TBalius: /* Information on number_save and number_write parameters */

2017-11-15T00:18:02Z

Information on number_save and number_write parameters

← Older revision		Revision as of 00:18, 15 November 2017
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	== Information on number_save and number_write parameters ==		== Information on number_save and number_write parameters ==

			This is true for DOCK v3.7.1rc1 (and later versions).

	"number_save" is the number that are minimized and written to OUTDOCK.		"number_save" is the number that are minimized and written to OUTDOCK.

TBalius: /* Information on number_save and number_write parameters */

2017-11-14T23:48:04Z

Information on number_save and number_write parameters

← Older revision		Revision as of 23:48, 14 November 2017
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	We recommended setting these numbers to 1 for production run discovery campaigns.		We recommended setting these numbers to 1 for production run discovery campaigns.
	we topically only modify number_save/number_write to 10 if you want to perform more exhaustive sampling for a small number (e.g. less than 1000) of molecules.		we topically only modify number_save/number_write to 10 if you want to perform more exhaustive sampling for a small number (e.g. less than 1000) of molecules.

			[[File:Miminizer.2017.11.14.png\|thumb\|center\|500px\|how resulting poses will very with different values of number_save and number_write]]

TBalius at 19:28, 14 November 2017

2017-11-14T19:28:39Z

← Older revision		Revision as of 19:28, 14 November 2017
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	To initiliaze the simplex, this iseed number used to generate a random number. e.g. used for trn and rotstep calc		To initiliaze the simplex, this iseed number used to generate a random number. e.g. used for trn and rotstep calc
	iseed 777		iseed 777


			== Information on number_save and number_write parameters ==

			"number_save" is the number that are minimized and written to OUTDOCK.

			"number_write" are the number that are written to the mol2 file.

			For example, if you set number_save to 10 and number_write to 2 then 10 poses will be minimized but only the top two scoring minimized poses will be written out to the mol2 file.


			The parameters (number_save/number_write) are applied to each db2 hierarchy. Each protomer/tautomer has one or more db2 hierarchies. So if there are multiple protonation state each will have the "number_write" poses written out to the mol2 file (caveat, dock might not generate that many in which case it will write all that are possible).

			We recommended setting these numbers to 1 for production run discovery campaigns.
			we topically only modify number_save/number_write to 10 if you want to perform more exhaustive sampling for a small number (e.g. less than 1000) of molecules.

Enkhjargal at 20:48, 17 March 2017

2017-03-17T20:48:59Z

← Older revision		Revision as of 20:48, 17 March 2017
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	sim_itmax 500		sim_itmax 500

	This is the initial distance in angstroms the molecule is translated. (This is used to initiliaze the simplex)		This is the initial distance in angstroms the molecule is translated (In Angstrom). (This is used to initiliaze the simplex)

	sim_trnstep 0.2		sim_trnstep 0.2

	How many degrees of initial rotation are done. (This is used to initiliaze the simplex)		How many degrees of initial rotation are done (In Degree). (This is used to initiliaze the simplex)

	sim_rotstep 5.0		sim_rotstep 5.0

	If the energy changes by this much, restart the minimizer from this newest position.		If the energy changes by this much, restart the minimizer from this newest position. Between 2 subseq runs: if energy changes by more than 1kcal restart minimizer from latest position for another round.
	sim_need_to_restart 1.0		sim_need_to_restart 1.0

	How much the total energy can changed to be considered converged. Setting this higher will stop faster, setting it lower will cause it to do more iterations before converging (or potentially hitting the iteration max above).		How much the total energy can changed to be considered converged. within one run: considered converged when energies of lowest and highest energy state differ by only 0.1kcal/mol. Setting this higher will stop faster, setting it lower will cause it to do more iterations before converging (or potentially hitting the iteration max above).
	sim_cnvrge 0.1		sim_cnvrge 0.1

	Don't minimize molecules that score above ~~the min_cut~~.		Don't minimize molecules that score above this large number.
	min_cut 1.0e15		min_cut 1.0e15

	To initiliaze the simplex, this iseed number used to generate a random number.		To initiliaze the simplex, this iseed number used to generate a random number. e.g. used for trn and rotstep calc
	iseed 777		iseed 777

Enkhjargal at 23:27, 15 November 2016

2016-11-15T23:27:08Z

← Older revision		Revision as of 23:27, 15 November 2016
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	sim_itmax 500		sim_itmax 500

	This is the initial distance in angstroms the molecule is translated.		This is the initial distance in angstroms the molecule is translated. (This is used to initiliaze the simplex)

	sim_trnstep 0.2		sim_trnstep 0.2

	How many degrees of initial rotation are done.		How many degrees of initial rotation are done. (This is used to initiliaze the simplex)

	sim_rotstep 5.0		sim_rotstep 5.0

Enkhjargal at 23:16, 15 November 2016

2016-11-15T23:16:18Z

← Older revision		Revision as of 23:16, 15 November 2016
Line 39:		Line 39:
	min_cut 1.0e15		min_cut 1.0e15

	To initiliaze the simplex, this ~~seed gets~~ used to generate a random number.		To initiliaze the simplex, this iseed number used to generate a random number.
	iseed 777		iseed 777

Enkhjargal at 23:15, 15 November 2016

2016-11-15T23:15:45Z

← Older revision		Revision as of 23:15, 15 November 2016
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	~~the~~ best scored ligand conformation can be minimized using the following parameters.		The best scored ligand conformation can be minimized using the following parameters.

			Add following section to existing INDOCK after SCORING section.

	#####################################################		#####################################################

Enkhjargal: Created page with "the best scored ligand conformation can be minimized using the following parameters. ##################################################### # MINIMIZATIO..."

2016-11-15T23:12:30Z

Created page with "the best scored ligand conformation can be minimized using the following parameters. ##################################################### # MINIMIZATIO..."

New page

the best scored ligand conformation can be minimized using the following parameters.

#####################################################
# MINIMIZATION
minimize yes
sim_itmax 500
sim_trnstep 0.2
sim_rotstep 5.0
sim_need_to_restart 1.0
sim_cnvrge 0.1
min_cut 1.0e15
iseed 777

The default for minimize is no. Yes turns on the minimization.
minimize yes

How many iterations of minimization to do. More means longer run times, but potentially better poses.

sim_itmax 500

This is the initial distance in angstroms the molecule is translated.

sim_trnstep 0.2

How many degrees of initial rotation are done.

sim_rotstep 5.0

If the energy changes by this much, restart the minimizer from this newest position.
sim_need_to_restart 1.0

How much the total energy can changed to be considered converged. Setting this higher will stop faster, setting it lower will cause it to do more iterations before converging (or potentially hitting the iteration max above).
sim_cnvrge 0.1

Don't minimize molecules that score above the min_cut.
min_cut 1.0e15

To initiliaze the simplex, this seed gets used to generate a random number.
iseed 777