Protonated state for HIS

1

Hi,
I am trying to dock a protein-peptide structure. Both have HIS. I did not assign the protonated state; therefore, they should all be double protonated. However, this is the case only in the protein.
In the peptide- I start with an HD1 and when the docking starts, the begin file changes to HE2.
How can this be? why are they not both protonated?
Of course I have set delenph=false

Thank you

2

Because the server automatically defined the protonation state based on the hydrogen bonding (using the reduce software from molprobity).

At expert level you can manually define the protonation state.

3

I am using the local version 2.4
Is this the case there too?

4

You need to manually define the protonation state in run.cns for each his of each molecule.

5

I know, but if I don’t define it then it should be double-protonated, no?
So I don’t understand why that is not always the case
(the HIS is far from the binding zone so it is not critical what state it is in so I did not spend the time defining it- but I want to know why HADDOCK is not making it double protonated)

6

Actually there is an automatic mode:


{==================== histidine patches =====================}
{* Automatically define histidine protonation state based on energetics *}
{===>} autohis=true;

it basically evaluate all three possibilities and takes the protestation state that give the best electrostatic energy.

You should turn it off if you want to manually change things (or have them all protonated by default)