ADL: Histidine

MOUSUMI PAUL mousumi45 at
Thu Jun 20 12:20:56 PDT 2013

I have faced same problem before. and I follow this link..

Here are a couple of possible ways to deal with HIP,HID and HIE in ADT.

(1) The simplest is to set a user preference "adt_editHISprotonation".
By default, this user preference is set to "No change".  Other choices
are "HD1", "HE2" and "HD1HE2" which govern which hydrogens appear on the
histidine residues.... You can set this user preference in ADT via
File->Preferences->Modify Defaults which opens a "Set User Preferences"
widget.... Scroll down until you see "adt_editHISprotonation", click on
the down aroow to show the other options, click on the one you want and
then click on Set.... and possible on "make default" if you want to use
a certain protonation state for every HIS in every receptor you format
for autodock in ADT..

(2) You can interactively set the protonation state of individual HIS
residues using a command in the Pmv/repairCommands module.
(NOTE: Do this AFTER you have added hydrogens !!)
   (A) First you must load this module:
           File->Browse Commands
           click on Pmv under "Select a package"
           scroll down until  you see  repairCommands and click on it
           click on "Load Module" and "DISMISS"
   (B) Now "Edit Histidine Hydrogens" is available in the  menu
displayed by clicking on Edit->Hydrogens.
   (C) Clicking on Edit->Hydrogens->Edit Histidine Hydrogens opens a
widget listing each histidine present in the current selection (or in
the viewer if there is nothing currently selected)  followed by 3
radiobuttons in columns labelled  "0,HD1", "0, HE2" and "+1"  The first
choice is to have "HD1" only on the histidine which would give it a
total charge of 0. The second is to have "HE2" only on the histidine
which would give it a total charge of 0.  The last is to put both of
them on the histidine, giving it a total charge of +1.  You set the
pattern of protonation as you wish and then click on "Apply".  ADT will
then add or remove hydrogens according to the pattern you have set with
the radiobuttons.....[It can be a bit time-consuming]....

hope this help to solve your problem.


On Thu, Jun 20, 2013 at 2:46 PM, Mezei, Mihaly <mihaly.mezei at>wrote:

> Greetings,
> I noticed that if I have a HIS residue ADT makes it protonated with adding
> polar hydrogens only. If I rename HIS to HIE, I get the same result. If I
> rename HIS to HSD I gen an error. So, how can I control the protonation
> state of histidines?
> Thanks, regards,
> Mihaly Mezei
> Department of Structural and Chemical Biology, Icahn School of Medicine at
> Mount Sinai
> Voice:  (212) 659-5475   Fax: (212) 849-2456
> WWW (MSSM home):
> WWW (Lab home - software, publications):
> WWW (Department):
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