AMBER Archive (2006)

Subject: AMBER: problem with calcpka.pl

From: Benjamin Juhl (itbbju_at_itb.uni-stuttgart.de)
Date: Tue Oct 24 2006 - 06:58:27 CDT

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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