Re: [AMBER] Further question on protonation state of histidine

From: Brian Radak <>
Date: Fri, 6 Apr 2012 09:02:38 -0400

Hi Acoot,

I'm pretty sure leap will only automatically build protons based on residue
names, whether some are there or not. I believe standard neutral residues
are labeled HIS and +1 residues are labeled HIP. Neutral residues with
epsilon protonation are HIE. Of course all of that can be quickly verified
using xleap.

As for assigning protonation states, I don't know what the AMBER standard
protocol is. There must be a program for doing that based off empirical
pKas in AmberTools somewhere and I'm sure someone else more knowledgeable
than me will reply by the end of the day.


On Fri, Apr 6, 2012 at 7:25 AM, Acoot Brett <> wrote:

> Dear All,
> For low resolution structure PDB, the protonation state of histidine is
> not clear. Then should we correct our PDB file manually so that leap can
> get the correct imput filesd? Or leap treat the protonation state of HIS
> automatically?
> Even for high resolution structure of protein, the protonation state of
> HIS is usallly unclear or unspefified. Do we have some rules to correct the
> protonation state of the residues including HIS? Or there is a server for
> this purpose?
> Cheers,
> Acoot
> _______________________________________________
> AMBER mailing list

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 Brian Radak                                             :     BioMaPS
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Received on Fri Apr 06 2012 - 06:30:19 PDT
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