AMBER Archive (2004)

Subject: Re: AMBER: histidine and its various forms

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 18 2004 - 09:58:44 CST

On Wed, Feb 18, 2004, Stern, Julie wrote:
>
> I need to name a histidine that doesn't have a hydrogen
> on either the delta nitrogen or the epsilon nitrogen. Just
> using HIS defaults to HID which is the name for protonation
> on the delta position. HIE is the name for protonation on
> the epsilon position. HIP is the name for protonation on
> both positions. But, what would I call or how would I do
> a workaround for protonation on neither position?
>

There is no standard residue for this situation. You would have to create
one, probably by modifying HID or HIE to remove a proton, then calculating
new charges. You can name it whatever 3-letter name you want.

...good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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