It's not readily apparent to me what was changed in those directions, but
that seems to have done the trick.
Thanks for the help,
Brian
On Sun, May 25, 2014 at 10:44 PM, Robert Konecny <rok.ucsd.edu> wrote:
> Hi Brian,
>
> symlinking should work just fine, just make sure you do 'make clean && make
> depend' in $AMBERHOME/AmberTools/src/sander before running 'make -e
> AMBERBUILDFLAGS="-DAPBS" $AMBERHOME/bin/sander.APBS'.
>
> I'm including instructions for compiling iAPBS with Amber14, I'll update
> the online docs soon.
>
> Best,
>
> Robert
>
>
> On Sun, May 25, 2014 at 11:17:43AM -0400, Brian Radak wrote:
> > I made the following changes to the protocol at that link:
> >
> > 1) Since I already have a perfectly good install of Amber14, I did not
> > unpack the source code into the iAPBS build directory, but rather just
> made
> > a symlink instead (does this directory *need* to be called amber12 as
> > implied by the instructions?).
> >
> > 2) Since the sander source code no longer exists in AMBERHOME/src but
> > instead AMBERHOME/AmberTools/src, I changed to this directory instead
> when
> > linking in the apbs*.F90 files.
> >
> > When I finally get to the "make" stage, everything goes well for a few
> > seconds and then I get this error:
> >
> > =======
> > gfortran -DMKL -DBINTRAJ -DEMIL -DAPBS -DAPBS -c -O0 -ffree-form
> > -I../pbsa -I../sqm -I../rism -I../../../include
> > -I/home/radakb/iapbs/amber12/include -I/home/radakb/iapbs/amber12/include
> > -I/u2/opt/intel/Compiler/11.1/072/mkl/include -DAPBS -DAPBS -DRISMSANDER
> -o
> > apbs.APBS.o apbs.F90
> > apbs.F90:21.8:
> >
> > USE apbs_vars
> > 1
> > Fatal Error: Can't open module file 'apbs_vars.mod' for reading at (1):
> No
> > such file or directory
> > make: *** [apbs.APBS.o] Error 1
> >
> > =======
> >
> > I tried compiling apbs_vars.F90 with a similar command and then "make"
> > again, but that just created less helpful errors (I think undefined
> > variables, etc.)
> >
> > Did I really mess something up with the symlink procedure above? It seems
> > silly to have multiple copies of Amber source all over the place.
> >
> > Thanks,
> > Brian
> >
> >
> >
> > On Sat, May 24, 2014 at 10:54 PM, Robert Konecny <rok.ucsd.edu> wrote:
> >
> > > Hi Brian,
> > >
> > > iAPBS should work fine with Amber14 too - what error messages are you
> > > getting?
> > >
> > > Thanks,
> > >
> > > Robert
> > >
> > > On Fri, May 23, 2014 at 04:54:06PM -0400, Brian Radak wrote:
> > > > I'm trying to compile the sander/APBS interface using the directions
> > > found
> > > > here:
> > > >
> > > > http://mccammon.ucsd.edu/iapbs/doc/amber.html
> > > >
> > > > but I seem to be getting errors with module files not getting made.
> Since
> > > > these instructions are for AMBER12, I assume that there are problems
> > > > related the sander source code getting moved to AmberTools. Has
> anyone
> > > > tried this after the new AMBER release?
> > > >
> > > > Thanks,
> > > > Brian
> > > >
> > > > --
> > > > ================================ Current Address
> =======================
> > > > Brian Radak :
> BioMaPS
> > > > Institute for Quantitative Biology
> > > > PhD candidate - York Research Group : Rutgers, The State
> > > > University of New Jersey
> > > > University of Minnesota - Twin Cities : Center for
> > > Integrative
> > > > Proteomics Room 308
> > > > Graduate Program in Chemical Physics : 174 Frelinghuysen
> Road,
> > > > Department of Chemistry : Piscataway,
> NJ
> > > > 08854-8066
> > > > radak004.umn.edu :
> > > > radakb.biomaps.rutgers.edu
> > > > ====================================================================
> > > > Sorry for the multiple e-mail addresses, just use the institute
> > > appropriate
> > > > address.
> > > > _______________________________________________
> > > > 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
> > >
> >
> >
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > 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
>
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
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Received on Tue May 27 2014 - 06:00:02 PDT
