AMBER Archive (2004)

Subject: Re: AMBER: AMBER 8 default is now HIS->HIE and not HIS->HID - typo?

From: David A. Case (case_at_scripps.edu)
Date: Thu Oct 28 2004 - 11:50:34 CDT

On Tue, Oct 26, 2004, Chris Moth wrote:

> In the AMBER 8 distribution we are running at Vanderbilt, all the
> $AMBERHOME/dat/leap/cmd/leaprc.ff* files now end with:
>
> ==========================================================
> #
> # assumed that most often proteins use HIE
> #
> NHIS = NHIE
> HIS = HIE
> CHIS = CHIE
> ==========================================================
>
> which now makes HIE the default when LEAP reads a HIS residude in a .pdb.
>
> Page 48 of the AMBER 8 manual still refers to the AMBER 7 behavior however,
> "...The default "leaprc" file assigns the name HIS to HID. Thus, if a PDB
> file is read that contains the residue HIS, the residue will be assigned to
> the HID UNIT object...."

Thanks for the note. I have posted an erratum on the Amber web page.
>
> Also, would you mind sharing your reasoning for the change? Do you have a
> new literature reference for frequency of HIE vs HID?

Most histidines are actually HIE. I am on the road right now, and don't have
an exact reference, but the Structural Biochemistry book by Jack Kyte gives
a nice explanation of these tautomeric issues.

...thanks...dac

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