Hi Phil -

You're correct on the results from APBS - apparently I missed that line when updating the tutorial.  I get a value of 19.963 kJ/mol, which looks to match the results you've obtained.  I'll make the changes to the documentation shortly.

As for the asc_getToken error, this really does not effect APBS at all as it is a MALOC error - so you can safely ignore it.

I'd also like to add (for the general APBS populace as well) that if you'd like to check whether your self-compiled version of APBS is working correctly, we've recently added test cases for the examples in the aptly-named examples/ directory.  Please see the examples/README.html file for more information on running these tests.

Thanks for bringing this to my attention!


On 1/18/06, Martin, Philip <pmartin@med.wayne.edu > wrote:
I have recently installed apbs on three machines. An AMD x86_64 athlon and x86_64 dual CPU opteron on which I compiled both maloc and apbs myself (with the x86_64 BLAS library) running Centos V4.2, and on a P4 from the maloc and apbs RPM's running Fedora Core 2.

While going through the protein kinase tutorial I get the following error:

martin@gort [protein_kinasa_a] #39 > apbs apbs-energy.in > apbs-energy.out
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.

In following the links I fount that the error was supposed to be caused by no END card at the end of the pqr files. Adding the END line still didn't repair the error.

But what is very disturbing is that on all three machines I'm getting numbers that agree with one another are very different from the reported numbers in the binding energy tutorial (shown below).

print energy 3 (complex) - 2 (pka) - 1 (bal) end
  Local net energy (PE 0) = 1.996285144649E+01 kJ/mol
  Global net energy = 1.996285144649E+01 kJ/mol

The tutorial indicates I should get a binding energy of 5.8 kJ/mol. Am I doing something wrong? I followed the tutorial exactly, downloading all the files directly off the web site.

Phil Martin

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