I got a “Your HADDOCK run has encountered errors and was aborted” message (job number 15467, https://wenmr.science.uu.nl/haddock2.4/run/7968502472/E9-A20-C). The water refinement step of it1 and the subsequent analysis/clustering were not performed. I wonder whether this is due to the explicit solvent = true statement, resulting in a much too large number of water molecules ? I am looking at a complex between a proteins of roughly 1000 and 125 residues …
If this were the case, could it be possible to change this statement and rerun the refinement and analysis only without starting from the beginning ?
CNS analysis files in it1/analysis already exist.
To rerun the analysis delete the “DONE” file in the analysis directory.
starting water refinement for the 200 best structures regarding energy
starting DOCKING protocol
Traceback (most recent call last):
File “/home/enmr/software/haddock2.4-grid/Haddock/RunHaddock.py”, line 700, in
File “/home/enmr/software/haddock2.4-grid/Haddock/Main/MHaddock.py”, line 310, in ForAllIterations
currstatus = status[statusroot + str(strucID)]
Cleaning up HADDOCK run directory
Only files for structure #1 will be kept…
And there is also an error in complex_run1_it1_refine_1.out:
HEAP: maximum use = 3023048728 current use = 1536000 bytes
HEAP: maximum overhead = 7360 current overhead = 1232 bytes
Maximum dynamic memory allocation: 3023048728 bytes
Maximum dynamic memory overhead: 7360 bytes
Program started at: 20:35:42 on 03-Jul-2020
Program stopped at: 20:54:22 on 03-Jul-2020
CPU time used: 1106.1976 seconds