AMBER Archive (2004)

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

From: Chris Moth (Chris.Moth_at_vanderbilt.edu)
Date: Tue Oct 26 2004 - 15:24:05 CDT

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...."

I checked around the reflector and your manual corrections page and did not
see this mentioned... So, I thought I should bring the typo to your
attention.

Also, would you mind sharing your reasoning for the change? Do you have a
new literature reference for frequency of HIE vs HID?

Thanks

Chris