AMBER Archive (2006)

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

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Tue Jul 11 2006 - 11:00:58 CDT

The output is normal.

You may want to follow the example input in the manual,
for example, constant temperature (after heating), ntc=ntf=2, and tol= .. etc

You have too many titrable sites.
I think that's why you decrease the dt and ntcnstph.
In addition, you may want to exlcude TYR and LYS for acidic and GL4 and AS4 for
basic simulations.

On 7/11/06, Guillaume Bollot <Guillaume.Bollot_at_chiorg.unige.ch> wrote:
> 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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-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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