AMBER Archive (2006)

Subject: Re: AMBER: problem with calcpka.pl

From: David A. Case (case_at_scripps.edu)
Date: Sun Oct 29 2006 - 22:33:54 CST

> Date: Wed, 25 Oct 2006 17:14:20 -0700
> From: "John Mongan"
> Subject: Re: AMBER: problem with calcpka.pl
>
> You seem to have run 100 ps of simulation at a single pH value. This
> is not nearly sufficient sampling to get optimum predictions, even
> within the (significant) limitations of the force-field and GB model.
> The sampling regimen (1 ns at every 0.5 pH across the pKa range of
> interest) used in the JCC paper referenced in the manual should
> probably be considered a bare minimum for sampling, and more would
> certainly be needed if your system is particularly flexible.
>
> Constant pH methods are still somewhat in their infancy and there are
> many potential pitfalls. If you haven't read the paper describing the
> method, I would strongly recommend that you do so prior to investing
> much time with the method (though as the author I'm somewhat
> biased...)
>
> Hope this helps,
>
> John
>
> On 10/24/06, Benjamin Juhl <itbbju_at_itb.uni-stuttgart.de> wrote:
> > Dear all,
> >
> >
> > i was interested on the effect of different pH values on a lipase i am
> > studying and wanted to use the simulations at constant pH as described
> > in the manual (chapter 6.11 - Amber9).
> > When i want to analyse the protonation states of some residues from the
> > cpout files with calcpka.pl i get following output at a ph=7:
> >
> > AS4 6: Offset 1.549 Pred 8.549 Frac Prot 0.973 Transitions 2
> > AS4 17: Offset 1.546 Pred 8.546 Frac Prot 0.972 Transitions 2
> > AS4 49: Offset 1.966 Pred 8.966 Frac Prot 0.989 Transitions 16
> > AS4 75: Offset 1.514 Pred 8.514 Frac Prot 0.970 Transitions 6
> > GL4 81: Offset 2.157 Pred 9.157 Frac Prot 0.993 Transitions 12
> > AS4 126: Offset -2.558 Pred 4.442 Frac Prot 0.003 Transitions 2
> > AS4 134: Offset 2.299 Pred 9.299 Frac Prot 0.995 Transitions 2
> > AS4 145: Offset 2.467 Pred 9.467 Frac Prot 0.997 Transitions 2
> > AS4 187: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
> > GL4 188: Offset 1.095 Pred 8.095 Frac Prot 0.926 Transitions 55
> > AS4 200: Offset 2.162 Pred 9.162 Frac Prot 0.993 Transitions 2
> > AS4 223: Offset 0.656 Pred 7.656 Frac Prot 0.819 Transitions 94
> > HIP 224: Offset 0.980 Pred 7.980 Frac Prot 0.905 Transitions 84
> > AS4 252: Offset 1.139 Pred 8.139 Frac Prot 0.932 Transitions 40
> > AS4 257: Offset 1.851 Pred 8.851 Frac Prot 0.986 Transitions 20
> > AS4 265: Offset 0.578 Pred 7.578 Frac Prot 0.791 Transitions 116
> > GL4 269: Offset 1.191 Pred 8.191 Frac Prot 0.939 Transitions 48
> > GL4 294: Offset -1.982 Pred 5.018 Frac Prot 0.010 Transitions 6
> > AS4 296: Offset 1.253 Pred 8.253 Frac Prot 0.947 Transitions 34
> > Can't call method "ResName" on an undefined value at
> > /share/apps/amber9_lampath/exe/calcpka.pl line 65.
> >
> > The shown pKa values are very unrealistic and i wonder if this could be
> > due to the error in the calcpka.pl script and would appreciate any help.
> >
> >
> > I used the following input file for the analysed part of the simulation:
> > &cntrl
> > igb=1, cut=30.0, ig = 12703,
> > imin=0, ntx=5, irest=1, ntpr=100, ntwx=200, ntwr=100,
> > ntc=2, tol=0.00000001, ntb=0, ntp=0,
> > tautp=2.0,
> > nstlim=100000, dt=0.001, ntr=0,
> > temp0=300.0, ntt=1,
> > ntf=2,
> > icnstph = 1, solvph = 7, ntcnstph = 2,
> > scee = 1.2, saltcon = 0.1, nrespa = 1,
> > /
> >
> >
> > Thanks,
> > Benjamin Juhl
> > -----------------------------------------------------------------------
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> >
> >

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