Hi,
OK, it seems that you're missing 2 libraries, libapbs_routines.a and
libiapbs.a. I would suggest retrying step 2.2 in
http://mccammon.ucsd.edu/iapbs/doc/amber.html#_building_iapbs_interface
and make sure the build completes successfully. It may be helpful to
redirect stderr to a file during the build so you can more easily find
error messages.
-Dan
On Thu, Sep 5, 2013 at 11:40 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
> it gives:
>
> libapbs_generic.so libapbs_mg.so libapbs_pmgc.so libmaloc.so
>
>
> On Thu, Sep 5, 2013 at 11:03 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> 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
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> AMBER.ambermd.org
> 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 - 11:00:06 PDT
