# Error with solvent refinement **URL:** \ **Category:** HADDOCK\ **Created:** [July 6, 2020, 9:17am UTC](https://ask.bioexcel.eu/t/error-with-solvent-refinement/2308 "2020-07-06T09:17:22Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![beate](https://avatars.discourse-cdn.com/v4/letter/b/85f322/32.png) [@beate](https://ask.bioexcel.eu/u/beate)\ **Post date:** [July 6, 2020, 9:17am UTC](https://ask.bioexcel.eu/t/error-with-solvent-refinement/2308/1 "2020-07-06T09:17:22Z")
Bonjour 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](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 ? Thanks, Beate Haddock.out says 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 run[‘haddock\_dir’], run) File “/home/enmr/software/haddock2.4-grid/Haddock/Main/MHaddock.py”, line 310, in ForAllIterations currstatus = status[statusroot + str(strucID)] KeyError: ‘wpdb\_265’ 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 ============================================================ ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [July 6, 2020, 9:30am UTC](https://ask.bioexcel.eu/t/error-with-solvent-refinement/2308/2 "2020-07-06T09:30:39Z")
Hi Beate There is a “feature” we are working on that causes a problem when the number of water models is less than the it1 models. Is this the case for your system? A temporary solution is to set the number of water refined models equal to the number of it1 models, until the problem is fixed. ---
**Author:** ![beate](https://avatars.discourse-cdn.com/v4/letter/b/85f322/32.png) [@beate](https://ask.bioexcel.eu/u/beate)\ **Post date:** [July 6, 2020, 9:47am UTC](https://ask.bioexcel.eu/t/error-with-solvent-refinement/2308/3 "2020-07-06T09:47:58Z")
Hi Alexandre Yes, probably, see below … (in the meantime I realized that it0 did not go into the refinement with the same error message). I am submitting an NMR ensemble of 20 structures (I could reduce to 10, they are really well-resolved). Therefore, I was told to set the number of structures for the rigid body docking to something around 4000 (200 docking trials per structure). Maybe this is overshooting ? What would you suggest ? I am profiting from this message to ask you an additional question: I have NOE restraints between the two partners that I would like to use. They are mainly between methyl groups and aromatics. Now, how do you deal with what in Aria requires the “or” command HD11 or HD12 or HD13, (for example) while CNS also accepts HD1# ? Or you rather advice to use carbon atoms with additional pseudoatom corrections ? Thanks Beate {\* Setting for the rigid-body (it0) and semi-flexible refinement (it1) \*} {\* number of structures for rigid body docking _} {===\>} structures\_0=4000; keepstruct\_0=&structures\_0; {_ number of structures for refinement _} {===\>} structures\_1=400; keepstruct\_1=&structures\_1; keepstruct\_2=&structures\_1; {_ number of structures to be analysed\*} {===\>} anastruc\_1=200; anastruc\_0=&anastruc\_1; anastruc\_2=&anastruc\_1; ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [July 6, 2020, 10:07am UTC](https://ask.bioexcel.eu/t/error-with-solvent-refinement/2308/4 "2020-07-06T10:07:25Z")
Hi Beate > I am submitting an NMR ensemble of 20 structures (I could reduce to 10, they are really well-resolved). Therefore, I was told to set the number of structures for the rigid body docking to something around 4000 (200 docking trials per structure). Maybe this is overshooting ? What would you suggest ? 4000/400/400 is fine in this case. (And the feature should be solved). > I have NOE restraints between the two partners that I would like to use. They are mainly between methyl groups and aromatics. Now, how do you deal with what in Aria requires the “or” command HD11 or HD12 or HD13, (for example) while CNS also accepts HD1# ? Or you rather advice to use carbon atoms with additional pseudoatom corrections ? HD1# will work, no pseudoatom correction required since we are using a (Sum[1/r**6])**(-1/6) to calculate the effective distance. And if you define NOEs to protons, make sure to keep all hydrogens as HADDOCK removes the non-polar ones by default. ---
**Author:** ![beate](https://avatars.discourse-cdn.com/v4/letter/b/85f322/32.png) [@beate](https://ask.bioexcel.eu/u/beate)\ **Post date:** [July 6, 2020, 10:08am UTC](https://ask.bioexcel.eu/t/error-with-solvent-refinement/2308/5 "2020-07-06T10:08:26Z")
Thank you, I will submit a new job ! Have a nice summer ! Beate