Qnifft DOCK 3.6 conversion - Revision history

Therese: 10 revisions

2012-10-08T20:32:22Z

10 revisions

← Older revision

Revision as of 20:32, 8 October 2012

2012-02-13T21:08:52Z

← Older revision		Revision as of 21:08, 13 February 2012
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	Qnifft is a new option for use instead of DelPhi with DOCK 3.6 It is a poisson boltzmann solver program from Kim Sharp [[http://crystal.med.upenn.edu/software.html]]. It has been integrated into the [[DOCK Blaster]] and [[DOCK 3.6]] toolchain. For now if you make use of it, please cite:		Qnifft is a new option for use instead of DelPhi with DOCK 3.6 It is a poisson boltzmann solver program from Kim Sharp [[http://crystal.med.upenn.edu/software.html]]. It has been integrated into the [[DOCK Blaster]] and [[DOCK 3.6]] toolchain. For now if you make use of it, please cite:

	Sharp, K. A. 1995. Polyelectrolyte electrostatics: Salt dependence, entropic and enthalpic contributions to free energy in the nonlinear Poisson-Boltzmann model. Biopolymers 36:227-243. [http://10.1002/bip.360360210 10.1002/bip.360360210]		Sharp, K. A. 1995. Polyelectrolyte electrostatics: Salt dependence, entropic and enthalpic contributions to free energy in the nonlinear Poisson-Boltzmann model. Biopolymers 36:227-243. [http://dx.doi.org/10.1002/bip.360360210 10.1002/bip.360360210]

	and		and

2011-12-22T18:07:12Z

← Older revision		Revision as of 18:07, 22 December 2011
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	Once you have the new phimap, you have to edit your INDOCK to point to it instead of the old phimap (rec+sph.phi usually). Once you've done that, you also have to use the new DOCK executable located in $DOCK_BASE/bin/Linux/dock.csh The best way to use this is to use the following command instead of $mud/submit.csh:		Once you have the new phimap, you have to edit your INDOCK to point to it instead of the old phimap (rec+sph.phi usually). Once you've done that, you also have to use the new DOCK executable located in $DOCK_BASE/bin/Linux/dock.csh The best way to use this is to use the following command instead of $mud/submit.csh:

	$mud/subdock.csh $DOCK_BASE/bin/Linux~~/dock3.6_qnifft~~/dock.csh		$mud/subdock.csh $DOCK_BASE/bin/Linux/dock.csh

	This should produce compatible OUTDOCK & test.eel1.gz files.		This should produce compatible OUTDOCK & test.eel1.gz files.

2011-12-22T18:06:56Z

← Older revision		Revision as of 18:06, 22 December 2011
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	make autonew		make autonew

	Once you have the new phimap, you have to edit your INDOCK to point to it instead of the old phimap (rec+sph.phi usually). Once you've done that, you also have to use the new DOCK executable located in $DOCK_BASE/bin/Linux~~/dock3.6_qnifft~~/dock.csh The best way to use this is to use the following command instead of $mud/submit.csh:		Once you have the new phimap, you have to edit your INDOCK to point to it instead of the old phimap (rec+sph.phi usually). Once you've done that, you also have to use the new DOCK executable located in $DOCK_BASE/bin/Linux/dock.csh The best way to use this is to use the following command instead of $mud/submit.csh:

	$mud/subdock.csh $DOCK_BASE/bin/Linux/dock3.6_qnifft/dock.csh		$mud/subdock.csh $DOCK_BASE/bin/Linux/dock3.6_qnifft/dock.csh

2011-11-21T20:13:05Z

← Older revision		Revision as of 20:13, 21 November 2011
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	To produce new binaries for use with these grids.		To produce new binaries for use with these grids.

			== INDOCK file ==

			delphi_file ../../grids/rec+sph.qnifft.phi
			delphi_nsize 193

	== Backwards compatibility with the old grids ==		== Backwards compatibility with the old grids ==

2011-11-21T20:09:57Z

← Older revision		Revision as of 20:09, 21 November 2011
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	== Backwards compatibility with the old grids ==		== Backwards compatibility with the old grids ==

	~~See the section above on Recompiling DOCK 3.6 for the new Qnifft grids. Follow the steps described~~, ~~except change the nsize~~ parameter ~~from 193~~ to 179. This is the ~~backwards compatibility with the old~~ grids.		Edit your INDOCK file, add a delphi_nsize parameter and set it to 179. This allows use of old delphi grids instead of the 193 sized Qnifft grids.

	[[Category:DOCK]]		[[Category:DOCK]]

2011-11-14T23:38:28Z

← Older revision		Revision as of 23:38, 14 November 2011
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	See the section above on Recompiling DOCK 3.6 for the new Qnifft grids. Follow the steps described, except change the nsize parameter from 193 to 179. This is the backwards compatibility with the old grids.		See the section above on Recompiling DOCK 3.6 for the new Qnifft grids. Follow the steps described, except change the nsize parameter from 193 to 179. This is the backwards compatibility with the old grids.

			[[Category:DOCK]]

2011-11-09T21:06:22Z

← Older revision		Revision as of 21:06, 9 November 2011
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	To produce new binaries for use with these grids.		To produce new binaries for use with these grids.

			== Backwards compatibility with the old grids ==

			See the section above on Recompiling DOCK 3.6 for the new Qnifft grids. Follow the steps described, except change the nsize parameter from 193 to 179. This is the backwards compatibility with the old grids.

2011-10-19T17:25:58Z

compilation

← Older revision		Revision as of 17:25, 19 October 2011
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	$mud/subdock.csh $DOCK_BASE/bin/Linux/dock3.6_qnifft/dock.csh		$mud/subdock.csh $DOCK_BASE/bin/Linux/dock3.6_qnifft/dock.csh

			This should produce compatible OUTDOCK & test.eel1.gz files.

			== Recompiling DOCK 3.6 to use the new Qnifft grids ==

			If you're using a different version of DOCK 3.6 and want to change it to be compatible with Qnifft-produced grids, you only have to change one line. In max.h change

			parameter (nsize=179)

			to

			parameter (nsize=193)

			Then you have to run

			cd i386 ; make clean ; make ; make SIZE=32

			To produce new binaries for use with these grids.

2011-10-19T17:23:06Z

finished first draft?

← Older revision		Revision as of 17:23, 19 October 2011
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	make autonew		make autonew

	Once you have		Once you have the new phimap, you have to edit your INDOCK to point to it instead of the old phimap (rec+sph.phi usually). Once you've done that, you also have to use the new DOCK executable located in $DOCK_BASE/bin/Linux/dock3.6_qnifft/dock.csh The best way to use this is to use the following command instead of $mud/submit.csh:

			$mud/subdock.csh $DOCK_BASE/bin/Linux/dock3.6_qnifft/dock.csh