Docking of small ssDNA on proteins

HADDOCK
1

Hello,

I am trying to do a docking of multiple small (6 nts) single-stranded DNAs on a protein. I am wondering if I am using the right parameters. I would like to dock blindly. Here is a part of my cfg file with the parameters i found online.

[topoaa]
autohis = true

[rigidbody]
tolerance = 5
ambig_fname = “”
sampling = 10000
surfrest = true
epsilon = 78
dielec = “cdie”
randremoval = false
w_desolv = 0

[caprieval]

[seletop]
select = 400

[flexref]
tolerance = 5
ambig_fname = “”
epsilon = 78
dielec = “cdie”
randremoval = false
w_desolv = 0
dnarest_on = false
tadfactor = 4

[caprieval]

[emref]
tolerance = 5
ambig_fname = “”
randremoval = false
dnarest_on = false
w_desolv = 0
contactairs = true

[caprieval]

[emscoring]

[caprieval]

Thanks you very much,

Marc-Antoine

2

A few suggested changes (and you might consider adding some clustering step at the end)

3

Hello @amjjbonvin,

Thanks for the answers, but I don’t see your suggested changes.

Thanks again,

Marc-Antoine

4

Must have been filtered out from my email answer… Here it comes:

#=====================

[topoaa]

[rigidbody]
tolerance = 5
sampling = 10000
cmrest = true
epsilon = 78
dielec = “cdie”
w_desolv = 0

[caprieval]

[seletop]

select = 400

[flexref]
tolerance = 5
epsilon = 78
dielec = “cdie”
w_desolv = 0

contactairs = true

tadfactor = 4

[caprieval]

[emref]
tolerance = 5
w_desolv = 0

[caprieval]

#=====================

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