Re: [AMBER] HID or HIE which one to consider?

From: <>
Date: Wed, 10 Sep 2014 12:19:13 +0530

Hi Marc,

Thank you so much for your suggestion. I checked my structure using H++
server which assign some of the HIS as HIE and some as HID. Actually, it
is a DNA binding protein. So I would like to keep HIS state correctly. The
exact DNA interacting residues are not known.

For MD simulation, is it ok to keep the protonation status as defined by
H++ server or should I keep the default one where all HIS are made to HIE?

With regards,

> One of the (important, IMO) jobs of setting up a protein system for
> simulation is deciding on the protonation state and most likely tautomers
> (HIE or HID) of the HIS residues.
> HIE is more common in proteins, I believe, BUT you should check for EACH
> histidine which state is most likely.
> There are numerous tools that can help you with this.
> A non-exhaustive list of some of them:
> pdb2pqr (just google)
> reduce (part of AmberTools)
> H++ server (see
> WHAT-IF optimum hydrogen bond network tool (see
> If a HIS is in an important place for what you want to study and the
> protonation/tautomer isn't clear from the structure, you may want to
> consider trying HID, HIE (and if applicable HIP).
> Hope this helps,
> Marc
> On 8 September 2014 14:34, <> wrote:
>> Dear users,
>> AMBER by default makes HIS to HIE which is neutral and hydrogen is on
>> the
>> epsilon nitrogen. But if we look at the stability among the three forms
>> at
>> pH=7 (close to physiological pH) HID > HIE > HIP.
>> HID is also neutral and hydrogen is on the delta nitrogen. Most of the
>> literature use HIE.
>> Which one is more accurate to take for the simulation, HID or HIE?
>> With regards,
>> Sunita
>> _______________________________________________
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Received on Wed Sep 10 2014 - 00:00:03 PDT
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