AMBER Archive (2006)

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

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Fri Jul 07 2006 - 11:14:42 CDT

No problem.

To find the mid-point, you should increase the solvent pH.

On 7/7/06, Guillaume Bollot <Guillaume.Bollot_at_chiorg.unige.ch> wrote:
> 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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-- 
Best wishes,

MYUNGGI YI
==================================
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Institute of Molecular Biophysics
Florida State University
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Office: (850) 645-1334
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