On Tue, 2014-03-04 at 11:12 +0200, Ahmet yıldırım wrote:
> Dear users,
>
> How can I get/find the Amber force field parameters for the deprotonated
> histidine?
Histidine has 3 major protonation states at biological pHs.
Single-protonated at the delta- or epsilon- positions and
double-protonated (protonated at both). The first two states are
neutral, the third is positively charged.
You have to change the residue name of HIS to HIE or HID for epsilon- or
delta-protonated histidine, respectively (HIS is interpreted as HIE).
To get the double-protonated form, change the residue name to HIP.
A fully deprotonated histidine (no protons on either Ne or Nd) would
need to be parametrized (mainly just the charge derivation). See
http://ambermd.org/tutorials/advanced/tutorial1_orig/ for example. Note
that this is a _highly_ unusual form of histidine that would only be
present at extremely high pHs (I've never seen the pKa value for the
second imidazole H since it rarely [ever??] comes off).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 04 2014 - 05:30:03 PST
