Rescoring with PLOP - Revision history

Frodo at 00:53, 11 March 2014

2014-03-11T00:53:59Z

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	[[Category:Tutorials]]		[[Category:Tutorials]]
	~~[[Category:PLOP]]~~

Frodo at 16:13, 14 February 2014

2014-02-14T16:13:02Z

← Older revision		Revision as of 16:13, 14 February 2014
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	Once it done, we can take a look together.		Once it done, we can take a look together.

	[[Category:~~Tutorial~~]]		[[Category:Tutorials]]
	[[Category:PLOP]]		[[Category:PLOP]]

Frodo at 04:14, 14 February 2014

2014-02-14T04:14:50Z

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	then all the individual jobs should be submitted to queue automatically.		then all the individual jobs should be submitted to queue automatically.
	Once it done, we can take a look together.		Once it done, we can take a look together.

			[[Category:Tutorial]]
			[[Category:PLOP]]

Therese: 1 revision

2012-10-08T20:32:22Z

1 revision

← Older revision

Revision as of 20:32, 8 October 2012

JohnIrwin at 19:06, 27 September 2007

2007-09-27T19:06:49Z

New page

Instruction for rescoring:

On broadway, copy niu's .tchrc to your directory, make sure you are also
using tcsh, not csh or bsh.

1. receptor structure preparation

first, run ~nhuang/scripts/nwdock_pdb_fix rec.pdb rec.new
compare the original rec.pdb and rec.new to make sure rec.new has chain
name. then move rec.new to rec.pdb.

copy ~nhuang/scripts/rec_h_opt.con, delete the "template ..." line if
there has no cofactor.

you can prepare the receptor file either by running PLOP in queue or
interactively. I recommend the later one.

Check which node is free by run "checknodes", then login the free one
(assume 15) by "ssh klient15"

go to the right directory and run "echo rec_h_opt.con | ~nhuang/plop/plop
&"

Note, weird thing going on if you run it directly from broadway headnode
which not suppose to be, however, for safety reason not kicked out of
broadway, DO LOG INTO CLIENT NODE to run PLOP jobs.

2. ligand parameters files generation

On broadway headnodes, if test.eel1.gz (known ligands) and s_.new.eel1.gz
(decoys or whatever) in current directory, run "prep_templates_qgen
jobname", a file named jobname.que will be generated, take a look what
inside; then do "qsub jobname.que".

for 25,000 ligands, it takes ~ one day to generate parameter files and
return one file "jobname.tar.gz".

You may want to check what's inside this package, or not.

3. on Baton2

scp the rec_h_opt.pdb, rec_h_opt.log and jobname.tar.gz to Baton2, untar
the tar file, and make sure the directories are consistent (check
/ccpr1/nhuang/testcase/new/thrombin_opls/, the subdirectory ligands and
mddr_decoys)

run "super_submit_2006.csh jobname opls/amsol &"

then all the individual jobs should be submitted to queue automatically.
Once it done, we can take a look together.