Hi,
What is the result of 'ls $APBS_LIBDIR'?
-Dan
On Thu, Sep 5, 2013 at 11:25 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
> Hi..
>
> I tried to do what you suggested...but now the error message is changed...i
> am getting some missing library routines notice..
>
> ================================================
> gfortran -DBINTRAJ -DAPBS -ffree-form -I../../AmberTools/src/pbsa
> -I../../AmberTools/src/sqm -I../../AmberTools/src/rism -I../../include
> -I/usr/local/softs/iapbs_build/amber12/include
> -I/usr/local/softs/iapbs_build/amber12/include -DAPBS -DAPBS -o
> sander.APBS file_io_dat.APBS.o apbs_vars.APBS.o apbs.APBS.o constants.o
> state.o memory_module.o stack.o nose_hoover.o nose_hoover_vars.o
> nose_hoover_init.o trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o
> icosasurf.o egb.o remd.o findmask.o relax_mat.o nmr.o multitmd.o
> multisander.o sander.APBS.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o
> printe.APBS.o runmin.o rdparm.o mdread.APBS.o locmem.o runmd.o getcor.o
> degcnt.o decnvh.o fastwt.o parallel.o shake.o ene.o mdwrit.o minrit.o set.o
> dynlib.APBS.o mdfil.o nmlsrc.o ew_force.o ew_setup.o ew_box.o ew_bspline.o
> ew_fft.o nonbond_list.o short_ene.o ew_recip.o pcshift.o align.o csa.o
> rfree.o rgroup.o amopen.o debug.o ew_recip_reg.o ew_handle_dips.o
> ew_dipole_recip.o mexit.o new_time.o extra_pts.o thermo_int.o matinv.o
> assert.o mmtsb.o mmtsb_client.o erfcfun.o constantph.o prn_dipoles.o ips.o
> sglds.o iwrap2.o emap.o amoeba_valence.o amoeba_multipoles.o amoeba_recip.o
> amoeba_interface.o amoeba_direct.o amoeba_mdin.o amoeba_adjust.o
> amoeba_self.o amoeba_vdw.o amoeba_induced.o amoeba_runmd.o bintraj.o
> binrestart.o spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o
> linear_response.o molecule.o xref.o dssp.o charmm.o crg_reloc.o
> sander_lib.o amd.o qm_mm.o qm_ewald.o qmmm_vsolv.o qm2_extern_module.o
> qm2_extern_adf_module.o qm2_read_adf_results.o KFReader.o ArrayList.o
> qm2_extern_gms_module.o qm2_extern_tc_module.o qm2_extern_gau_module.o
> qm2_extern_orc_module.o qm2_extern_nw_module.o qmmm_adaptive_module.o
> prn_qmmm_dipole.o \
> pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o cmd_matrix.o
> lscivr_vars.o lsc_init.o lsc_xp.o force.APBS.o \
> -L/usr/local/softs/iapbs_build/lib -liapbs -lapbs_routines
> -lapbs_mg -lapbs_generic -lapbs_pmgc -lmaloc -lz \
> -L/usr/local/softs/iapbs_build/amber12/lib -lsqm -lFpbsa \
> ../lib/nxtsec.o ../lib/sys.a ncsu-abmd-hooks.o
> ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o ncsu-colvar.o
> ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-utils.o ncsu-constants.o
> ncsu-cv-ANGLE.o ncsu-cv-COM_ANGLE.o ncsu-cv-COM_DISTANCE.o
> ncsu-cv-COM_TORSION.o ncsu-cv-COS_OF_DIHEDRAL.o ncsu-cv-DISTANCE.o
> ncsu-cv-HANDEDNESS.o ncsu-cv-LCOD.o ncsu-cv-MULTI_RMSD.o
> ncsu-cv-N_OF_BONDS.o ncsu-cv-N_OF_STRUCTURES.o ncsu-cv-R_OF_GYRATION.o
> ncsu-cv-TORSION.o ncsu-lexer.o ncsu-parser.o ncsu-pmd-hooks.o ncsu-rmsd.o
> ncsu-sander-hooks.o ncsu-sander-proxy.o ncsu-cv-PCA.o ncsu-read-pca.o
> ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o mt19937.o
> /usr/local/softs/iapbs_build/amber12/lib/libnetcdf.a \
> -larpack -llapack -lblas \
> -DAPBS -DAPBS
> /usr/bin/ld: cannot find -liapbs
> /usr/bin/ld: cannot find -lapbs_routines
> collect2: error: ld returned 1 exit status
> make: *** [sander.APBS] Error 1
> =============================================
>
> P.S. : i have created APBS_LIBDIR and APBS_LIBS variables as mentioned in
> the link below:
> http://mccammon.ucsd.edu/iapbs/doc/amber.html#_building_iapbs_interface
>
> Thanks
>
>
> On Thu, Sep 5, 2013 at 9:27 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
>> On Thu, Sep 5, 2013 at 11:27 AM, Asmita Gupta <asmita4des.gmail.com>
>> wrote:
>>
>> > yes, i did that
>> >
>> > make clean
>> > make depend
>> > make -e AMBERBUILDFLAGS="-DAPBS" sander.APBS
>> >
>>
>> Try:
>>
>> make -C $AMBERHOME clean
>> make depend
>> make -e AMBERBUILDFLAGS="-DAPBS" sander.APBS
>>
>> instead and see if that works.
>>
>>
>>
>> >
>> > and then i ended up with the error
>> >
>> >
>> > On Thu, Sep 5, 2013 at 7:51 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>> >
>> > > Hi,
>> > >
>> > > On Thu, Sep 5, 2013 at 12:35 AM, Asmita Gupta <asmita4des.gmail.com>
>> > > wrote:
>> > > > Fatal Error: Wrong module version '0' (expected '9') for file
>> > >
>> > > Did you 'make clean' first?
>> > >
>> > > -Dan
>> > >
>> > > --
>> > > -------------------------
>> > > Daniel R. Roe, PhD
>> > > Department of Medicinal Chemistry
>> > > University of Utah
>> > > 30 South 2000 East, Room 201
>> > > Salt Lake City, UT 84112-5820
>> > > http://home.chpc.utah.edu/~cheatham/
>> > > (801) 587-9652
>> > > (801) 585-9119 (Fax)
>> > >
>> > > _______________________________________________
>> > > 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
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Sep 05 2013 - 11:00:02 PDT
