View source for Rescoring with PLOP

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.

[[Category:Tutorials]]