Re: [AMBER] Regarding the protonation states of Histidine

From: Soumendranath Bhakat <>
Date: Thu, 11 Jun 2015 10:13:13 +0200

Use H++ server to see the pka values of all your histidines. If the pKa
value is very much above 7 say for example 8 or above or less than 7 say
for 6 and below then H++ server will adjust the protonation states
automatically. If it is in the border line say for example within the range
6.5 to 7.2 then you have to manually look into those histidnes and see if
there is chance of protonation for those histidines (check the H++ output
carefully in case of those borderline residues).

In VMD you can see those histidnes and neighbouring residues using
command *within
5 of resid <id here>*

the H++ output gives the name HIS to all residues despite adding correct
protonation. But you can rename the residues to the following keeping in
mind their protonation states using the output of H++ server

   - HID - histidine neutral δ-protonated
   - HIE - histidine neutral ε-protonated
   - HIS - histidine neutral (HID and HIE combined)
   - HIP - histidine positive protonated on both sidechain nitrogens

Also check the cysteine residues if it is bridged or normal CYS.

All the best.


On Thu, Jun 11, 2015 at 8:50 AM, muhammad tahir ayub <>

> Today I extracted pdb file from the RCSB protein data bank, No hydrogen's
> were present, when the proton were added to the protein through MOE
> software, it added the Hydrogen to the epsilon position to all HISTIDINE
> residues in pdb file.
> How can i come to the true protonation state of the HISTIDINE residue for
> my pdb file ( PDB ID : 4KIK )
> *Muhammad Tahir*
> *Ayub*
> *Junior Research Fellow*
> *H.E.J Research Institute of Chemistry*
> _______________________________________________
> AMBER mailing list

Thanks & Regards;
Soumendranath Bhakat
Research Assistant, Division of Biophysical Chemistry, CMPS, Lund
University, Sweden
Google Scholar:
Past: Molecular Modelling and Drug Design Research Group
Discipline of Pharmaceutical Sciences
UKZN, Westville
and Department of Pharmaceutical Sciences
Birla Institute of Technology, Mesra, India
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Received on Thu Jun 11 2015 - 01:30:02 PDT
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