Make a directory and include the following files:
- 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.
/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.
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:
LIGAND_START 5001 (this line is not included in the XP_1.in file as it starts from the beginning)
MAXREF 800RINGCONFCUT 2.500000
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:
Apple cluster run-command:
/opt/schrodinger/glide your_XP_file.in -HOST xgrid-server