AMBER Archive (2006)

Subject: AMBER: Amber8.0 predictied pKa problem for a Lysine!

From: Guillaume Bollot (Guillaume.Bollot_at_chiorg.unige.ch)
Date: Fri Jul 07 2006 - 04:38:08 CDT

Hello,
I have a problem with a predicted pKa value for lysine residue (it's the
for the tyrosine) after constant pH (5.0) simulation.
This is my calcpKa.pl log file :

LYS 137: Offset Inf Pred Inf Frac Prot 1.000 Transitions 2
GL4 160: Offset 2.201 Pred 7.201 Frac Prot 0.994 Transitions 3
LYS 161: Offset Inf Pred Inf Frac Prot 1.000 Transitions 0
GL4 164: Offset 0.210 Pred 5.210 Frac Prot 0.618 Transitions 43
GL4 168: Offset 1.456 Pred 6.456 Frac Prot 0.966 Transitions 1
LYS 172: Offset Inf Pred Inf Frac Prot 1.000 Transitions 0
AS4 174: Offset 1.535 Pred 6.535 Frac Prot 0.972 Transitions 13
TYR 176: Offset Inf Pred Inf Frac Prot 1.000 Transitions 0

what is INF or -INF values? is it normal?
Thank you very much 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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