Plop - Revision history

Frodo at 12:37, 21 March 2014

2014-03-21T12:37:29Z

← Older revision		Revision as of 12:37, 21 March 2014
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	= About PLOP =		= About PLOP =
	PLOP is a program by [[Matt Jacobson]] and his group at [[UCSF]] to perform [[:Category:Protein modeling \| protein modeling]]. It has also been used for [[ELC re-scoring]].		PLOP is a program by [[Matt Jacobson]] and his group at [[UCSF]] to perform [[:Category:Protein modeling \| protein modeling]]. It has also been used for [[ELC \|re-scoring]].
	Some documentation is available on the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group webpage].		Some documentation is available on the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group webpage].

Frodo at 12:37, 21 March 2014

2014-03-21T12:37:17Z

← Older revision		Revision as of 12:37, 21 March 2014
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	= About PLOP =		= About PLOP =
	PLOP is a program by [[Matt Jacobson]] and his group at [[UCSF]] to perform [[:Category:Protein modeling \| protein modeling]]. It has also been used for [[re-scoring]].		PLOP is a program by [[Matt Jacobson]] and his group at [[UCSF]] to perform [[:Category:Protein modeling \| protein modeling]]. It has also been used for [[ELC re-scoring]].
	Some documentation is available on the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group webpage].		Some documentation is available on the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group webpage].

Frodo at 12:36, 21 March 2014

2014-03-21T12:36:52Z

← Older revision		Revision as of 12:36, 21 March 2014
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	= About PLOP =		= About PLOP =
	PLOP is a program by [[Matt Jacobson]] and his group to perform [[protein modeling]]. It has also been used for [[re-scoring]].		PLOP is a program by [[Matt Jacobson]] and his group at [[UCSF]] to perform [[:Category:Protein modeling \| protein modeling]]. It has also been used for [[re-scoring]].
	Some documentation is available on the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group webpage].		Some documentation is available on the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group webpage].

			{{TOCright}}

	=Energy minimization using Plop=		=Energy minimization using Plop=

Frodo at 23:30, 11 March 2014

2014-03-11T23:30:08Z

← Older revision		Revision as of 23:30, 11 March 2014
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	[[Category:Software]]		[[Category:Software]]
	[[Category:~~Docking~~]]		[[Category:Protein Modeling]]

Frodo at 23:29, 11 March 2014

2014-03-11T23:29:50Z

← Older revision		Revision as of 23:29, 11 March 2014
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	[[Category:Software]]		[[Category:Software]]
	~~[[Category:Colleagues]]~~
	[[Category:Docking]]		[[Category:Docking]]

Frodo at 01:02, 11 March 2014

2014-03-11T01:02:50Z

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	[[Category:Software]]		[[Category:Software]]
	[[Category:Colleagues]]		[[Category:Colleagues]]
	[[Category:Docking ~~preparation~~]]		[[Category:Docking]]

Frodo at 01:01, 11 March 2014

2014-03-11T01:01:47Z

← Older revision		Revision as of 01:01, 11 March 2014
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	[[Category:Software]]		[[Category:Software]]
	~~[[Category:Protein modeling]]~~
	[[Category:Colleagues]]		[[Category:Colleagues]]
	[[Category:Docking preparation]]		[[Category:Docking preparation]]

Frodo at 15:49, 14 February 2014

2014-02-14T15:49:00Z

Frodo at 15:48, 14 February 2014

2014-02-14T15:48:20Z

← Older revision		Revision as of 15:48, 14 February 2014
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			= About PLOP =
			PLOP is a program by [[Matt Jacobson]] and his group to perform [[protein modeling]]. It has also been used for [[re-scoring]].
			Some documentation is available on the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group webpage].

	==Energy minimization using Plop==		==Energy minimization using Plop==
	This page describes simple protocols for receptor/active site and ligand minimization using Plop.<br>		This page describes simple protocols for receptor/active site and ligand minimization using Plop.<br>
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	[[Category:Protein modeling]]		[[Category:Protein modeling]]
	[[Category:Colleagues]]		[[Category:Colleagues]]
			[[Category:Docking preparation]]

Frodo at 04:07, 14 February 2014

2014-02-14T04:07:27Z

← Older revision		Revision as of 04:07, 14 February 2014
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	===Acknowledgements===		===Acknowledgements===
	Thanks to Jens, CK and Frank who introduced me to Plop. And to the Jacobson lab and Schroedinger.		Thanks to Jens, CK and Frank who introduced me to Plop. And to the Jacobson lab and Schroedinger.

			[[Category:Software]]
			[[Category:Protein modeling]]
			[[Category:Colleagues]]

← Older revision		Revision as of 15:49, 14 February 2014
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	Some documentation is available on the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group webpage].		Some documentation is available on the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group webpage].

	==Energy minimization using Plop==		=Energy minimization using Plop=
	This page describes simple protocols for receptor/active site and ligand minimization using Plop.<br>		This page describes simple protocols for receptor/active site and ligand minimization using Plop.<br>
	Check also the Plop manual on the Jacobson Wiki: http://wiki.jacobsonlab.org/index.php/Plop_manual <br><br>		Check also the Plop manual on the Jacobson Wiki: http://wiki.jacobsonlab.org/index.php/Plop_manual <br><br>
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	<br>		<br>

	===1. Add hydrogens to your ligand and convert to mol2 format===		==1. Add hydrogens to your ligand and convert to mol2 format==
	To run plop with a ligand, you need a template/parameter file for your ligand. To generate a template (section 2), you need a mol2 file with hydrogens. There are dozen of ways to add hydrogens (mostly absent in crystal structures) to your ligand. Whatever method you use (eg. convert.py, Chimera or Maestro for example), please check that the hydrogens are added correctly! Also check in the output mol2 file if all atoms have the right atom types. Ligands in crystal structures often have subtly incorrect geometries, which may confuse programs. I found adding hydrogens and conversion to mol2 format most reliable done with Maestro, but in most cases, you may simply use the following command: <br>		To run plop with a ligand, you need a template/parameter file for your ligand. To generate a template (section 2), you need a mol2 file with hydrogens. There are dozen of ways to add hydrogens (mostly absent in crystal structures) to your ligand. Whatever method you use (eg. convert.py, Chimera or Maestro for example), please check that the hydrogens are added correctly! Also check in the output mol2 file if all atoms have the right atom types. Ligands in crystal structures often have subtly incorrect geometries, which may confuse programs. I found adding hydrogens and conversion to mol2 format most reliable done with Maestro, but in most cases, you may simply use the following command: <br>

	convert.py --i=ML5.pdb --o=ML5.mol2 --add_hyd		convert.py --i=ML5.pdb --o=ML5.mol2 --add_hyd

	===2. Generate ligand template/parameter file for Plop===		==2. Generate ligand template/parameter file for Plop==
	Use plop_ff_params.csh to generate a template for Plop.		Use plop_ff_params.csh to generate a template for Plop.

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	Replace the ligand coordinates in your receptor with ML5.pdb and make sure that the template file (ml5) is the directory where you run plop. <br>		Replace the ligand coordinates in your receptor with ML5.pdb and make sure that the template file (ml5) is the directory where you run plop. <br>

	===3. Minimize protein and/or ligand using Plop===		==3. Minimize protein and/or ligand using Plop==

	Make a command file for plop (see example below) and run Plop: <br>		Make a command file for plop (see example below) and run Plop: <br>
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	A:301		A:301

	===Acknowledgements===		=Acknowledgements=
	Thanks to Jens, CK and Frank who introduced me to Plop. And to the Jacobson lab and Schroedinger.		Thanks to Jens, CK and Frank who introduced me to Plop. And to the Jacobson lab and Schroedinger.