Hi Oliver,

This seems to be related to something else (reading the dielectric maps in gz format). Can you send us an example (with pqr and apbs input files), so that we can reproduce such a problem?

Thanks,

Yong
 

On Tue, Nov 16, 2010 at 2:31 PM, Oliver Beckstein <oliver.beckstein@bioch.ox.ac.uk> wrote:
Hi Yong,

sorry for the delay in testing.

It's still not working for me: The files are read but then I get 0 for all volume integrals for every single file, e.g.

Got paths for 6 dielectric map sets
Reading x-shifted dielectric map data from dielx_prot_Lm.dx.gz:
 129 x 129 x 129 grid
 (1.95312, 1.95312, 1.95312) A spacings
 (-125.327, -122.628, -126.889) A lower corner
 Volume integral = 0.00e+00 A^3

Finally, the solver complains:

 Solving PDE (see io.mc* for details)...
% BUILDBAND: dpbfa problem:  1
% BUILDBAND: leading principle minor not PD...
% BUILDOPS: changing your MGSOLV
% BUILDOPS: to iterative...
% MVCS: rhs is zero on finest level
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
....

When gunzipping the files and reading in plain dx I get

Reading x-shifted dielectric map data from dielx_prot_Lm.dx:
 129 x 129 x 129 grid
 (1.95312, 1.95312, 1.95312) A spacings
 (-125.327, -122.628, -126.889) A lower corner
 Volume integral = 1.07e+09 A^3

The solver runs without problems.

(The dx.gz files were read noticably faster than the unzipped ones so I would very much like to be able to do everything with compressed files and they save 99% of diskspace.)

On 15 Nov, 2010, at 16:12, Yong Huang wrote:

> Thanks for reporting this, it was a bug in the APBS code, and it is now fixed in trunk. If you like, please check out a copy from APBS trunk (svn cohttps://apbs.svn.sourceforge.net/svnroot/apbs/trunk apbs ) and try it again.

I checked out r1622 from svn and compiled on Mac OS 10.6.2 with MacPorts:

./configure --prefix=/Users/oliver/Biop/Library/APBS/version/svn-`svnversion` --enable-python CC=gcc-mp-4.3 F77=gfortran-mp-4.3
make
make install

Best wishes,
Oliver

--
Oliver Beckstein
SBCB Unit, University of Oxford
email: oliver.beckstein@bioch.ox.ac.uk
web: http://sbcb.bioch.ox.ac.uk/oliver/