Hello everyone,
I’m a new user of HADDOCK seeking advice on configuring my protocol, especially for the itw steps (minimization and molecular dynamics).
My project focuses on studying alternative proteins derived from a bicoding transcript ( https://doi.org/10.1093/nar/gkad1050). I plan to perform protein-protein docking using HADDOCK3 locally. Since I lack experimental information and my structures are predicted by AlphaFold, I’m opting for an ab-initio docking approach.
Here are the main considerations for my protocol so far:
- I specified the center of mass as a distance restriction.
- I increased the number of generated structures from 1000 to 10000 for it0, and from 200 to 400 for it1 and itw.
- I changed the “number of partitions for random exclusion” from 2 to 1.1428. Should I use npart = 1.1428 ?
- For the minimization and molecular dynamics steps, I referred to the documentation available at the following link “Advanced refinement of molecular complexes – Bonvin Lab”, where it mentions “Number of MD steps …*4 → 0 for the 4 values (respectively 500/500/1000/1000 by default)”. Should I use these parameters (nemsteps= 500, waterheatsteps = 500, watersteps = 1000, watercoolsteps = 1000)?
Here’s what my configured config.cfg file looks like. Are these the appropriate parameters?
[topoaa]
#tolerance = 20
autohis = false
[it0 : rigidbody]
tolerance = 20
sampling = 10000
cmrest = true
cmtight = true
kcm = 1.0
ncs_on = false
ntrials = 1
npart = 1.1428
[it1 : flexref]
cmrest = true
cmtight = true
kcm = 1.0
ncs_on = false
max_nmodels = 400
npart = 1.1428
[itw : emref ]
npart = 1.1428
max_nmodels = 400
nemsteps = 500
timestep = 0.002
[itw : mdref]
max_nmodels = 400
solvent = ‘water’
nemsteps = 500
waterheatsteps = 500
watersteps = 1000
watercoolsteps = 1000
Thank you in advance for your advice and expertise.