Dear Amber users
I am performing 1NS of constant PH dynamics on a small, highly charged (+11)
peptide of 45 residues. I set up the initial input pdb file as stated in the
amber manual (i.e. I changed ASP to AS4, GLU to GL4). The constant pH ran
without problem. However, when I performed analysis on the output using
calcpka.pl I got the following message:
Can't call method "ResName" on an undefined value at
/opt/amber9/exe/calcpka.pl line 65.
When I looked at the resulting output from calcpka.pl nothing seemed to be
particularly wrong, except that I saw output from 10 residues and not the
expected 11. I also got this line:
GL4 28: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
Is the implication of this result that I should perform a more extended
dynamics run? How come there is no "predicted pka given" in the above
mentioned output?
My full calcpka.pl output is this:
LYS 8: Offset 2.465 Pred 9.465 Frac Prot 0.997 Transitions 144
TYR 9: Offset 2.167 Pred 9.167 Frac Prot 0.993 Transitions 254
TYR 10: Offset 1.638 Pred 8.638 Frac Prot 0.978 Transitions 430
LYS 26: Offset 2.935 Pred 9.935 Frac Prot 0.999 Transitions 34
GL4 27: Offset -3.886 Pred 3.114 Frac Prot 0.000 Transitions 8
GL4 28: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0
LYS 32: Offset 1.540 Pred 8.540 Frac Prot 0.972 Transitions 788
LYS 39: Offset 1.987 Pred 8.987 Frac Prot 0.990 Transitions 240
LYS 44: Offset 2.580 Pred 9.580 Frac Prot 0.997 Transitions 76
LYS 45: Offset 3.004 Pred 10.004 Frac Prot 0.999 Transitions
42
I would really appreciate some feedback on the matter.
Many thanks
Hayden Eastwood
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Received on Wed May 02 2007 - 06:07:15 PDT
