Hi, I want to run a water refinemet of a protein (44450 atoms) with a cofactor (50 to 100 atoms). I get an error message that the protein PDB exceed the maximum number of atoms allowed on this system, I would like to ask what is the limit of atoms in a system for the Refinemt interface?
Thank you,
Marija
The current limit on the 2.2 server is 50000 atoms.
Does your protein contain all hydrogens when you state 44450 atoms?
Thank you very much for your reply. No the initial strucutre which I submit does not contain hydrogens and after protonation there are for sure many more atoms than 50000.
I would like to ask you what is the atom limit in HADDOCK 2.4? And can I make only a minimization of the strucutre with the HADDOCK 2.4? Because my protein is a membrane protein and I wanted to have energy values for the protein-cofactor interaction after minimization step without subsequent water refinement.
Thank you very much
Hi Maria
The current limit also on 2.4 is 50000, but we will increase to 75000 (including hydrogens).
And the way to set it up is described at: https://www.bonvinlab.org/software/haddock2.4/tips/advanced_refinement/
By default the option to build the water shell is off and only a minimisation will be done.
Just increased to 75 000, could you try again? 
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