Sorry, I got the answer from the mail refelctor as written by D. Case.
Thanks,
----- Original Message -----
From: Jiten
To: amber.scripps.edu
Sent: Wednesday, October 05, 2005 1:21 AM
Subject: The default of HIS in leaprc : HID or HIE ?
Dear Amber users.
The default of HIS in leaprc in amber8 is HIE (it was HID in amber7). However, in amber8 manual it is mentioned that
Histidine can exist either as the protonated species or as a neutral species with a hydrogen at
the delta or epsilon position. For this reason, the histidine UNIT/RESIDUE name is either HIP,
HID, or HIE (but not HIS). 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. This feature can be changed within one's own "leaprc" file.
Which one is bettrer option for most proteins?
N. Jiten Singh
C/O Prof. Kwang S. Kim
Department of Chemistry
Pohang University of Science and Technology
San 31, Hyojadong, Namgu
Pohang 790-784, Korea
Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
Fax : 82-54-279-8137 (or +82-54-279-3399)
Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e
Home Page : http://www.geocities.com/njs_19
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Received on Tue Oct 04 2005 - 17:53:01 PDT
