Hi again Doug, sorry to be a bother hahah.
I used the top command to see what was going on as the calculation was being extremely slow and I realised some of my old ones were taking up CPU and memory. Once I removed those the calculation went on at usual speed.
In the middle of the night my laptop decided to update (just my luck) and so I restarted the calculation. Since it was most of the way through before it restarted (it had done 94/100) I tried the code using -gmds as the arguments as I didn't think it needed to redo the first steps since it had already done so. it also said "previous docking log files detected" and farmed out 6 jobs so I felt this confirmed I made an ok decision.
When I went to rank everything one of the files (number 9) seemed to not be right so I reran the script using all the arguments and this did the same thing (but farmed out one job - I believe since I reran the first arguments, the file for 9 was fixed and was able to perform the job on it) and I managed to get a completed output. From my understanding, this AutoDock step is simply scoring (as ranking becomes later) and so the order these molecules are docked is not important, so long as the correct .sdf file is used.
I ranked these using the script provided but I just wanted to double check that my process here appears logical or if I should delete all the files and redo the AutoDock docking?
I used the top command to see what was going on as the calculation was being extremely slow and I realised some of my old ones were taking up CPU and memory. Once I removed those the calculation went on at usual speed.
In the middle of the night my laptop decided to update (just my luck) and so I restarted the calculation. Since it was most of the way through before it restarted (it had done 94/100) I tried the code using -gmds as the arguments as I didn't think it needed to redo the first steps since it had already done so. it also said "previous docking log files detected" and farmed out 6 jobs so I felt this confirmed I made an ok decision.
When I went to rank everything one of the files (number 9) seemed to not be right so I reran the script using all the arguments and this did the same thing (but farmed out one job - I believe since I reran the first arguments, the file for 9 was fixed and was able to perform the job on it) and I managed to get a completed output. From my understanding, this AutoDock step is simply scoring (as ranking becomes later) and so the order these molecules are docked is not important, so long as the correct .sdf file is used.
I ranked these using the script provided but I just wanted to double check that my process here appears logical or if I should delete all the files and redo the AutoDock docking?