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Overcoming the Myths of the Review Process and Getting YourPaper Ready for Publication

3/6/2014

Journal of Physical Chemistry Editor Georg Schatz and his team outline the editorial review process and giving some guidelines for the reviewing process, responding to reviewer's comments, enhancing the readability during the revisions, etc.

http://pubs.acs.org/doi/pdf/10.1021/jz500162r

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Virtual Screening Workflow with the ZINC library on the apple cluster

3/6/2014

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SP
Make a directory and include the following files:

Example of SP.in file:
USECOMPMAE YES
NREPORT 30000
RINGCONFCUT 2.500000
GRIDFILE /home/eva/Zinc_screening/SP_1MV9/1MV9_no_wat_glide-grid.zip
LIGANDFILE /home/ZINC/druglike-Zinc-library-mol2/3_p0.0.mol2
LIGFORMAT mol2

Run the make_dirs script --> creates 88 folders (0-87)
Run the copy_files2 script --> leave the glide-dock_SP_0.in file out of its folder to run the script and when it is finished then cut+paste it to folder_0.
Use the submit_SP_all script to run the SP on apple cluster. In my case I used to put up to 12 jobs in each node ( modify this line of the script: for (( i = 76 ; i<=87; i++ )) ). Due to the fact that the jobs were put randomly to the nodes and in order to have up to 12 jobs on each node, I was using first some "fake" gromacs runs to use 12 cores and left the other 12 free for screening runs (Evi's idea! Thank's Evi!!).
When the run is finished you should check all the 88 directories and see if you have outputs like: e.g. glide-dock_SP_8_pv.maegz. If something goes wrong and the run has stopped then you will see e.g. glide-dock_SP_8_raw.maegz as an output. Then you should copy your glide-dock_SP_8.in to glide-dock_SP_8_b.in and run it from the ligand that it had stopped. Finally, you will have: glide-dock_SP_8_raw.maegz and glide-dock_SP_8_b_pv.maegz. Both are useful! Don't delete the first one!
In order to finish the SP process you have to take the top-scored 40.000 compounds from all the directories and put them to a new file (SP_top40000_1MV9_pv.maegz) to use as an input for the XP process.

You can run the GlideSortScript_ZINC.csh script to acheive this result. The content of the script is the following: (You have to add the possible raw.maegz files,too.)
/opt/schrodinger/utilities/glide_sort -n 40000 -o SP_top40000_1MV9_pv.maegz -r SP_top40000_1MV9.rept -hbond_cut 0.00 -cvdw_cut 0.00 -metal_cut 10.00 \ db3_p0.0/glide-dock_SP_0_pv.maegz \db3_p0.1/glide-dock_SP_1_pv.maegz \db3_p0.2/glide-dock_SP_2_pv.maegz \db3_p0.3/glide-dock_SP_3_raw.maegz \db3_p0.3/glide-dock_SP_3_b_pv.maegz \ etc.

XP
Each XP directory includes:

grid.zip file
SP_top40000_1MV9_pv.maegz (output of SP)
XP.in files (I split them into 8 files in my case)

Example of XP.in file:
WRITEREPT YES
WRITE_RES_INTERACTION YES
WRITE_XP_DESC YES
USECOMPMAE YES
POSTDOCK_NPOSE 10
LIGAND_END 10000
LIGAND_START 5001 (this line is not included in the XP_1.in file as it starts from the beginning)
MAXREF 800RINGCONFCUT 2.500000
GRIDFILE /home/eva/XP_Zinc/1MV9_XP_Zinc_2_8/1MV9_no_wat_glide-grid.zip
LIGANDFILE /home/eva/XP_Zinc/1MV9_XP_Zinc_2_8/SP_top40000_1MV9_pv.maegz
PRECISION XP

So, I split it to 8 XP directories:
0 - 5000, 5001 - 10000, 10001 - 15000, ..., 35001 - 40000

Run each one on the cluster or on our PCs manually :
/opt/schrodinger/glide 1MVC_Zinc_XP1.in -HOST xgrid-server
/opt/schrodinger/glide 1MVC_Zinc_XP2.in -HOST xgrid-server etc.

Finally you take the top-scored 1000 compounds (as we did before for the SP process where we took the 40.000 top-scored ) using the same script (GlideSortScript_ZINC.csh):

/opt/schrodinger2012/utilities/glide_sort -n 1000 -o file_XP_1000_pv.maegz -r file_XP_1000_.rept -hbond_cut 0.00 -cvdw_cut 0.00 -metal_cut 10.00 glide-dock_XP_0_pv.maegz glide-dock_XP_1_pv.maegz glide-dock_XP_2_pv.maegz glide-dock_XP_3_pv.maegz glide-dock_XP_4_pv.maegz glide-dock_XP_5_pv.maegz glide-dock_XP_6_pv.maegz glide-dock_XP_7_pv.maegz glide-dock_XP_8_pv.maegz

Some useful tips:

Run faster with the -LOCAL flag:
/opt/schrodinger/glide -LOCAL file.in

path for ZINC on apple:
/Network/Servers/xgrid-Server.xgrid/Volumes/RAID/NetUsers/pgkeka/PI3K/Screening/ZINC/druglike-Zinc-library-mol2/

Apple cluster run-command:
/opt/schrodinger/glide your_XP_file.in -HOST xgrid-server

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Overcoming the Myths of the Review Process and Getting YourPaper Ready for Publication

Virtual Screening Workflow with the ZINC library on the apple cluster

Alexis, Michalis, Danai, Panos, Sotiris, Nastazia, Vassilis, Zoe

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