AMBER Archive (2009)

Subject: Re: [AMBER] Histidine, which form?

From: M. L. Dodson (activesitedynamics_at_comcast.net)
Date: Mon Jun 15 2009 - 11:45:25 CDT

On Jun 15, 2009, at 11:39 AM, Ross Walker wrote:

> Hi,
>
> Edit the residue name in the pdb. If it is HIS I 'think' it defaults
> to epsilon. The residue names to use are:
>
> HID = delta protonated
> HIE = epsilon protonated
> HIP = doubly protonated (+1 charge)
>
> All the best
> Ross

or, in leap, use loadPdbUsingSeq instead of loadPdb. I prefer this
way because I can edit my leap script to change his forms (or other
changes) instead of having to muck with the pdb file.

Bud Dodson

>
>
>> -----Original Message-----
>> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
>> Behalf Of s. Bill
>> Sent: Monday, June 15, 2009 9:28 AM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] Histidine, which form?
>>
>> Dear Dr. Carlos / Ross
>> Thanks so much for your interest.
>> As you know, Hydrogens atoms are added by Xleap, so how can I
>> decide my
>> histadine which one of the three types?
>> I checked my PDB file, I found my histidine is not bonded throughout
>> imidazol ring. So, which form is it?
>> In other way, could you support me with three different examples,
>> please?
>> Thanks in Advance
>>
>> --- On Mon, 15/6/09, Carlos Simmerling <carlos.simmerling_at_gmail.com>
>> wrote:
>>
>> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
>> Subject: Re: [AMBER] Histidine, which form?
>> To: s_bill36_at_yahoo.co.uk, "AMBER Mailing List" <amber_at_ambermd.org>
>> Date: Monday, 15 June, 2009, 2:57 PM
>>
>> the delta N is the one closer to the alpha carbon- atoms are
>> labeled in
>> order alpha, beta, gamma, delta, epsilon moving out the side chain.
>> not
>> sure
>> what you mean by an example of HIP- this would be His at low pH. most
>> x=-ay
>> crystal structures have no H atoms so it is not clear which of the 3
>> forms
>> it really is. you need other experiments to tell.
>>
>>
>> On Mon, Jun 15, 2009 at 10:54 AM, <s_bill36_at_yahoo.co.uk> wrote:
>>
>>> Dear AMBER
>>> For Histidine, there are three forms of it, HIE, HID, and HIP.
>>> Delta poistion is position number 1 and Epsilon Position is position
>> number
>>> 3.
>>> The problem is that:
>>> There two different systems of numbering the atoms in the
>>> imidazole ring of histidine had both been used for a considerable
>> time
>>> (biochemists
>>> generally numbering as 1 the nitrogen atom adjacent to the side
>> chain, and
>>> organic chemists
>>> designating it as 3).
>>>
>>> So, could you tell me which nitrogen atom is the delta one, please?
>>> Also, could you give me an example of HIP when histidine is
>> protonated on
>>> both positions, please?
>>>
>>> Thanks in Advance
>>>
>>>
>>>
>>>
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-- 
M. L. Dodson
Business email: activesitedynamics-at-comcast-dot-net
Personal email: mldodson-at-comcast-dot-net
Phone: eight_three_two-five_63-386_one

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