Hi Abbie,
I think 100 dlg files per hour sounds OK. However, if Alistair sticks to mscoc1, you can use 16 cores on mscoc2 which will speed it up.
If you think it's still taking too long you could reduce the size of your library from 10,000 to 5,000.
Anyway, I've spotted yet another bug in the command I gave you to get the top 10,000 compound IDs out of the LIDAEUS output (apologies!). You actually need:
~douglas/scripts/docking/sdfgrep.ksh -l output.sdf | sed "s/_.*//" | awk '\!seen[$0]++'| head -10000 | sort -n > list.txt
(The 'sort -u' in the previous command actually changes the order of the IDs so you were no longer extracting the ones with the best LIDAEUS scores ...)
I realise this is my fault so if you need more time let me know and I can postpone the deadline by a few days.
Alistair could you please confirm you have seen this?
Doug
PS I attach instructions for using a program called Screen, to get around having to stay logged in all the time.