AMBER Archive (2006)

Subject: AMBER: Amber 8.0 no numerical value and offset for the predicted pKa of many titrable residue!!

From: Guillaume Bollot (Guillaume.Bollot_at_chiorg.unige.ch)
Date: Tue Jul 11 2006 - 06:19:29 CDT

Dear all,
I performed to constant pH simulation at 5.0 and 11.0 on my protein. When I
applied the calcpka.pl script on my cpout file, I have the following thing
(to pH= 11.0) :

GL4 1: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
AS4 17: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
HIP 31: Offset -3.036 Pred 7.964 Frac Prot 0.001 Transitions 1
TYR 33: Offset Inf Pred Inf Frac Prot 1.000 Transitions 611
TYR 41: Offset Inf Pred Inf Frac Prot 1.000 Transitions 2
LYS 44: Offset Inf Pred Inf Frac Prot 1.000 Transitions 19
LYS 50: Offset Inf Pred Inf Frac Prot 1.000 Transitions 85
TYR 54: Offset Inf Pred Inf Frac Prot 1.000 Transitions 4
LYS 55: Offset Inf Pred Inf Frac Prot 1.000 Transitions 7
AS4 65: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
AS4 75: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
LYS 79: Offset Inf Pred Inf Frac Prot 1.000 Transitions 33
GL4 84: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
GL4 86: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
AS4 87: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
TYR 91: Offset Inf Pred Inf Frac Prot 1.000 Transitions 0
HIP 98: Offset -2.250 Pred 8.750 Frac Prot 0.006 Transitions 1
TYR 101: Offset Inf Pred Inf Frac Prot 1.000 Transitions 0
LYS 108: Offset Inf Pred Inf Frac Prot 1.000 Transitions 53
GL4 110: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
LYS 112: Offset Inf Pred Inf Frac Prot 1.000 Transitions 59
AS4 115: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
GL4 119: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
LYS 121: Offset Inf Pred Inf Frac Prot 1.000 Transitions 142
GL4 123: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
GL4 124: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
LYS 137: Offset Inf Pred Inf Frac Prot 1.000 Transitions 45
GL4 160: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
LYS 161: Offset Inf Pred Inf Frac Prot 1.000 Transitions 267
GL4 164: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
GL4 168: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
LYS 172: Offset Inf Pred Inf Frac Prot 1.000 Transitions 115
AS4 174: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
TYR 176: Offset Inf Pred Inf Frac Prot 1.000 Transitions 0
HIP 179: Offset -2.251 Pred 8.749 Frac Prot 0.006 Transitions 1
TYR 180: Offset Inf Pred Inf Frac Prot 1.000 Transitions 17
GL4 182: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
LYS 185: Offset Inf Pred Inf Frac Prot 1.000 Transitions 13
LYS 187: Offset Inf Pred Inf Frac Prot 1.000 Transitions 5
AS4 193: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
AS4 194: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
LYS 196: Offset Inf Pred Inf Frac Prot 1.000 Transitions 11
TYR 200: Offset Inf Pred Inf Frac Prot 1.000 Transitions 4
GL4 209: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
AS4 210: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
TYR 214: Offset Inf Pred Inf Frac Prot 1.000 Transitions 0
TYR 215: Offset Inf Pred Inf Frac Prot 1.000 Transitions 0
LYS 217: Offset Inf Pred Inf Frac Prot 1.000 Transitions 1
TYR 219: Offset Inf Pred Inf Frac Prot 1.000 Transitions 0
TYR 221: Offset Inf Pred Inf Frac Prot 1.000 Transitions 12
TYR 225: Offset Inf Pred Inf Frac Prot 1.000 Transitions 0

Average total molecular protonation: 27.012
------------------------------------------

I don't really understand what happened? is it normal to have an INF (or
-INF) value? and what is this value? It's the for lysine residue for the
pH=5.0!!!
This is my input file :

md1_pH5.in: 100ps pH=11.0
&cntrl
icnstph=1, solvph=11.0, ntcnstph=2,
imin=0, igb=2, saltcon=0.1,
irest=0,
ntb=0,
cut=16,
tempi=0.0,
temp0=300.0,
ntt=1,
nstlim=100000, dt=0.001,
ntpr=100, ntwx=100, ntwr=100,
ntr=1,
&end
Restraint on 1AXTa
0.1
RES 1 236
END
END
-------------------------------------
Please help me!!!!
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

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