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.
> > > _______________________________________________
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> >
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> >
>
>
>
> --
> ================================ 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
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Received on Sun May 25 2014 - 20:00:02 PDT
