This script has a number of problems including a QUIT in the middle of
the script and a missing END statement for the PRINT block. These are
the causes of your problems; not the combination of polar and apolar
On Dec 19, 2007, at 5:39 AM, Amit wrote:
> I'm attaching the script that I used and the error message.
> CC: apbs-users@...
> From: baker@...
> To: amit1b@...
> Subject: Re: [Apbs-users] Binding
> Date: Tue, 18 Dec 2007 19:25:02 -0600
> Hello --
> 1. The tutorial script on protein-protein binding calculates the
> electrostatic free energy of binding (dG) by subtracting the
> energies of the individual proteins in water from that of the complex:
> This seems right and simple. However, I've seen in the literature
> other binding calculations, in which each of the above energies
> (protein A, protein B, complex) is calculated first as a dG, i.e. in
> relation to a vacuum reference state:
> ddG=dG(complex[water] - complex[vacuum]) - dG(A[water] - A[vacuum])
> - dG(B[water] - B[vacuum]).
> Are these equivalent?
> Yes, if the calculations are converged with respect to grid spacing
> (e.g., changing the grid spacing no longer changes the answer).
> If not, which of the two calculations would you consider more
> realistic physically/thermodynamically?
> In general, the first approach seems to usually be a bit more robust
> with respect to coarser grid spacings -- but this can be application-
> 2. Does anybody have a script which combines polar and apolar APBS
> calculations (either solvation or binding)? I seem to be able to do
> them separately but not at the same run.
> Really? What sort of failure are you encoutering? Can you send an
> example case that doesn't allow you to combine the two along with
> the output/error messages?
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> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
> Center for Computational Biology, Washington University in St. Louis
> Web: http://cholla.wustl.edu/
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> Xbox 360 Console. Get it now! <Solvation_focus_Elec_Apolar.in><Error
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis