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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Oct 28 2004 - 18:53:00 PDT
