Setting specific protonation states on amino acids other than histidine

HADDOCK
1

Hi there!

I have seen one can specify histidine protonation states in HADDOCK, but can one define protonation states for other amino acids? Turns out I’m working at pH 3 so even some of my proteins’ Asps and Glus are protonated, so I would like to switch off their negative charges.

Thanks in advance!

2

Hi Luciano

It is not possible, BUT we do have ASH and GLH residues defined in our force field, which would do the job.
So I can easily enable them in the portal, the only thing you will need to do it to change the residue name in the PDB file.

We will first test things on our side, and once working notify you.

Cheers
Alexandre

3

Hi Alexandre, yes, that will do the job.

OK I will wait for your notification.

Cheers

Luciano

4

Hi there

I can confirm that the protonated ASP and GLU are now supported by the HADDOCK2.2 web portal. The residue codes for these are ASH and GLH, respectively.

5

Super. Thanks!

Luciano