AMBER Archive (2006)

Subject: AMBER: Constant pH simulation : LYS residue

From: Guillaume Bollot (Guillaume.Bollot_at_chiorg.unige.ch)
Date: Tue Jul 04 2006 - 06:13:00 CDT

Dear Amber community,
I'm trying to determine the pKa of one lysine (resID : 217) in the active
site of my protein. I already performed a simulation (amber 8.0) at pH=5.0
and the problem is the following :
I used the utility calcpka.pl and for this lysine, the result is :

LYS 217: Offset Inf Pred Inf Frac Prot 1.000 Transitions 1

Is it normal? What is the Inf value?
I know that the pka reference for the lysine is 10.4 but I try to determine
the influence of the hydrophobe active site on this lysine.
Experimentaly, this lysine in this antibody should be neutral arond the pH
5 to 6 to do a nucleophilic attac.
This is my input for the equilibration :
&cntrl
icnstph=1, solvph=5.0, ntcnstph=2,
imin=0, igb=2, saltcon=0.1,
irest=0,
ntb=0,
cut=16,
tempi=0.0,
temp0=300.0,
ntt=1,
nstlim=50000, dt=0.001,
ntpr=50, ntwx=50, ntwr=50,
ntr=1,
&end
Restraint on 1AXTa
0.5
RES 1 236
END
END
----------------------
After I will perform next simulation with 2000ps and the same for pH 5.5,
6.0, 6.5 and 7.0. My input is correct?
My methodology is correct?

Thank a lot in advance.

BOLLOT Guillaume
Organic Chemistry Department
University of Geneva
30, quai Ernest-Ansermet
CH-1211 Geneva 4
tel. +41-22 379 6155
e-mail: Guillaume.Bollot_at_chiorg.unige.ch

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu