Frodo at 03:22, 14 February 2014

2014-02-14T03:22:13Z

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	* <code>-a</code> tells eplop to use an existing <code>plop.scores</code> file in the current folder and do not recalculate scores that already exist in that file. Please note that if you also set output file using <code>-o</code>, it will read from the designated output file instead of <code>plop.scores</code>.		* <code>-a</code> tells eplop to use an existing <code>plop.scores</code> file in the current folder and do not recalculate scores that already exist in that file. Please note that if you also set output file using <code>-o</code>, it will read from the designated output file instead of <code>plop.scores</code>.
	* <code>-v</code> and <code>-q</code> changes the verbosity of the script.		* <code>-v</code> and <code>-q</code> changes the verbosity of the script.


			[[Category:Internal]]
			[[Category:Docking]]
			[[Category:Tutorials]]

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2012-10-08T20:17:36Z

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==Overview==

eplop, or Easy PLOP, is a wrapper script for [[PLOP]]. It prepares the ligand and the receptor for use with PLOP, and can also invokes PLOP to performing [[re-scoring]]. There is option to turn on and off the ligand flexibility, and it could also save all working files so that you could manually tune the PLOP control file to perform more sophisticated analysis. The scoring output format is consistent with that of [[MUD - Michael's Utilities for Docking]] and [[SCORE]].

==Usage==

===The Simplest Approach===

Simply invoke <code>eplop</code> with paths to the receptor and the ligand:
~ycao/eplop/eplop receptor.pdb ligand.mol2
Note that the receptor structure must be in PDB format and that of the ligand must be in mol2 format. You may use <code>convert.py</code> to convert between different formats. Please be cautious when using <code>file2file.py</code>.

This will prepare the receptor using the '''first ligand''' in the <code>ligand.mol2</code> file, and then use the prepared receptor to score all ligands in the <code>ligand.mol2</code> file. The output will be written to the standard output as well as an output file named <code>plop.scores</code>.

===The Two-Step Approach===

Typically, you should prepare the receptor using the crystal ligand, and then use the prepared receptor to score the other ligands.

To prepare, run:
~ycao/eplop/eplop prepare receptor.pdb ligand.mol2
It will use only the first ligand in the <code>ligand.mol2</code> no matter how many ligands are present in that file. This will generated a PDB file whose name has a suffix <code>-prepared.pdb</code>. Now use that to score:
~ycao/eplop/eplop score receptor-prepared.pdb other-ligands.mol2

===Configuring the Scoring Methods===

If no methods are specified, the preparing step by default will add <code>opt yes</code> in the PLOP control file to prepare the protein, and the scoring step by default will assume ligand to be flexible using <code>minimize residue</code> in the PLOP control file. You could use the <code>--method</code> option to change the methods.

An alternative preparing method is <code>pka</code>, which uses <code>pka clust</code> in the PLOP control file. This is (much much) more time consuming, but may give you better results. For example:

~ycao/eplop/eplop prepare --method pka receptor.pdb ligand.mol2

Alternative scoring methods are <code>rigid</code>, which treats ligand as rigid and only changes its orientation, and <code>no_optim</code> which only performs energy calculation and no optimization using the given coordinates of ligands. For example:

~ycao/eplop/eplop score --method no_optim receptor.pdb ligand.mol2

If you are using the one-step simple approach to do both prepare and score, you could specify both the method of preparation and that of scoring:

~ycao/eplop/eplop --method pka:no_optim receptor.pdb ligand.mol2

or just the preparation method:

~ycao/eplop/eplop --method pka: receptor.pdb ligand.mol2

or just the scoring method:

~ycao/eplop/eplop --method :no_optim receptor.pdb ligand.mol2

===Useful Options===

All the options are very useful. Run
~ycao/eplop/eplop
to see a list of supported options. Here are some important ones.

* <code>-c</code> tells eplop to write the output in format compatible with Michael's script.
* <code>-s</code> tells eplop to save the pose of the ligands.
* <code>-p</code> tells eplop to keep the working directory. This is useful if you want to take a took at the log or the mol2 file containing the poses of ligands, or if you want to reuse the working directory to save time when used with <code>-d</code> options.
* <code>-o</code> tells eplop to write the score to an alternative file instead of standard <code>plop.scores</code>.
* <code>-a</code> tells eplop to use an existing <code>plop.scores</code> file in the current folder and do not recalculate scores that already exist in that file. Please note that if you also set output file using <code>-o</code>, it will read from the designated output file instead of <code>plop.scores</code>.
* <code>-v</code> and <code>-q</code> changes the verbosity of the script.

Eplop - Revision history

Frodo at 03:22, 14 February 2014

Therese: 6 revisions