Many thanks, Jason!
I now ran the AT15_Amber11.py script before building Amber11 and could
compile without problems.
I should have noted that myself...
Sorry things weren't idiot-proof enough yet for this idiot!
Tests run using 'make test' mostly ran ok. There were problems with Steered
and 'Pinned' MD tests, and I got messages like the following for
sander_pbsa_frc:
dbf_2.polyAT
Cannot match namelist object name cutres
namelist read: missplaced = sign
Cannot match namelist object name 5,
checking polyAT force
FAILED: polyAT force
In addition, there were also 'possible failures' for sander_pbsa_decres,
sander_pbsa_decpw as well as 02_MMPBSA_Stability, 03_MMPBSA_Binding.
The mdout.pbsa_decres.dif and mdout.pbsa_decpw.dif files showed only
marginal changes in the values (typically in the 3rd decimal
only). Differences in the MMPBSA test_statistics.out.dif files were somewhat
bigger (1st / 2nd decimal), but still not significant it seems. So I presume
I don't really have to worry about this.
If anyone has comments about these issues with testing (i.e. are they
expected, or do others see the same problems), they are welcome.
Marc
On 24 May 2011 13:38, Jason Swails <jason.swails.gmail.com> wrote:
> Did you run the AT15_Amber11.py script before trying to build Amber11?
>
> This error is fixed by that script. Furthermore, the configure script
> should say something about running that script before building amber.
>
> HTH,
> Jason
>
> On Tue, May 24, 2011 at 8:03 AM, Marc van der Kamp <
> marcvanderkamp.gmail.com
> > wrote:
>
> > Hi,
> >
> > Thanks for the reply.
> > My NetCDF configure did succeed,
> > with $AMBERHOME/AmberTools/src/netcdf_config.log exactly like you wrote,
> > without error messages.
> > I also have
> > NETCDF=netcdf.mod
> > NETCDFLIB=$(LIBDIR)/libnetcdf.a
> >
> > in my $AMBERHOME/AmberTools/src/config.h, followed by:
> > PNETCDF=no
> > PNETCDFLIB=
> >
> > I know I shouldn't have to do any extra linking or copying, but I just
> > wanted to try and see if it helped (as I didn't have any indications of
> > something else having gone wrong).
> > I will try and install both AmberTools 1.5 and AMBER 11 again, in a clean
> > directory.
> >
> > Thanks,
> > Marc
> >
> > On 24 May 2011 12:53, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > > Hi, it sounds like your netcdf might not have configured properly. My
> > > comments are below:
> > >
> > > On Tue, May 24, 2011 at 6:11 AM, Marc van der Kamp
> > > <marcvanderkamp.gmail.com> wrote:
> > > > When doing 'make serial', I first got the following error:
> > > >
> > > > cp ../../AmberTools/src/netcdf/include/*.mod .
> > > > cp: cannot stat `../../AmberTools/src/netcdf/include/*.mod': No such
> > file
> > > or
> > > > directory
> > > > make[1]: *** [netcdf.mod] Error 1
> > > >
> > > > It turned out that $AMBERHOME/AmberTools/src/netcdf/include didn't
> > exist,
> > >
> > > When you ran "$AMBERHOME/AmberTools/src/configure" did you get a
> > > message that "NetCDF configure succeeded"? Check near the end of
> > > $AMBERHOME/AmberTools/src/netcdf_config.log for any error messages. It
> > > should look something like:
> > >
> > > ...
> > > config.status: creating f90/Makefile
> > > config.status: creating examples/Makefile
> > > config.status: creating examples/C/Makefile
> > > config.status: creating examples/CDL/Makefile
> > > config.status: creating examples/CXX/Makefile
> > > config.status: creating examples/F90/Makefile
> > > config.status: creating examples/F77/Makefile
> > > config.status: creating config.h
> > > config.status: creating fortran/nfconfig1.inc
> > > config.status: executing depfiles commands
> > > ...
> > >
> > > Also, check your $AMBERHOME/AmberTools/src/config.h file. You should
> > > have two lines in it that read:
> > >
> > > NETCDF=netcdf.mod
> > > NETCDFLIB=$(LIBDIR)/libnetcdf.a
> > >
> > > > So I did 'make clean', and then made
> > > > the $AMBERHOME/AmberTools/src/netcdf/include directory with simlinks
> to
> > > > the $AMBERHOME/AmberTools/include/*mod files.
> > >
> > > You shouldn't have to do any extra linking or copying. At this point I
> > > would start with a clean directory, apply the bugfixes, the run
> > > configure and check all the output before attempting to make.
> > >
> > > -Dan
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 24 2011 - 07:00:02 PDT
