Multimer protein

[Vini161]

I am trying martini with go bias, with the webserver recommended: http://pomalab.ippt.pan.pl/GoContactMap/ . It gives 2 contact map output- go_contacts.txt and contact_map.out. The itp i get after using martinize is a single molecule0.itp. Will i need seperate chain itp for martini go like model? Do the inter and intra monomer potentials get defined by default?

[csbrasnett]

If you're using the latest version of martinize2, then you can use the go model by specifying -go contact_map.out, which will generate the contacts found from the file you gave to the server. There's some more documentation for the Go model options here but usually the defaults should work fine.

For multidomain proteins you may want to consider biasing any linking domains using the -water-bias flags (some more details here), which are detailed in the paper describing the Go model.

[Vini161]

Thank you! I am currently trying the latest Go-like model on a dimer. Is water-biasing mandatory for the simulation, or will the regular Go-like model suffice?

[csbrasnett]

That's likely to be highly system dependent, I'd recommend reading the paper I linked to understand more about the factors that make water-biasing necessary. In general for soluble proteins with disordered linking domains I'd recommend using the water biasing as described though.

[Vini161]

Thanks! I went through it and it is indeed relevant for my system, I did
martinize2 -f dimer.pdb -o topol.top -x cg_dimer.pdb -dssp -id-regions 1:26 362:388 -idr-tune -water-bias -water-bias-eps idr:0.5

I saw this in go_nbparams.itp
W molecule_0_1 1 0.47000000 0.50000000 ;water bias C
W molecule_0_2 1 0.47000000 0.50000000 ;water bias C
W molecule_0_3 1 0.41000000 0.50000000 ;water bias C
W molecule_0_4 1 0.41000000 0.50000000 ;water bias S
W molecule_0_5 1 0.47000000 0.50000000 ;water bias C
W molecule_0_6 1 0.47000000 0.50000000 ;water bias C
W molecule_0_7 1 0.47000000 0.50000000 ;water bias C
W molecule_0_8 1 0.47000000 0.50000000 ;water bias C
W molecule_0_9 1 0.41000000 0.50000000 ;water bias S
W molecule_0_10 1 0.41000000 0.50000000 ;water bias S
W molecule_0_11 1 0.47000000 0.50000000 ;water bias C
W molecule_0_12 1 0.47000000 0.50000000 ;water bias C
W molecule_0_13 1 0.41000000 0.50000000 ;water bias C
W molecule_0_14 1 0.41000000 0.50000000 ;water bias C
W molecule_0_15 1 0.41000000 0.50000000 ;water bias C
W molecule_0_16 1 0.41000000 0.50000000 ;water bias E
W molecule_0_17 1 0.47000000 0.50000000 ;water bias E

1. Just to clarify, it initially recognized residue 1 as C, but now it is treating it as water-biased after I defined it as IDR. Is that correct?
2. Is 0.5 (as suggested by tutorial) an acceptable value?