it could be an issue between ambertool11 and amber10 but on other OS
it seems to work fine.
On Thu, Jan 19, 2012 at 2:30 PM, Terry <terrencesun.gmail.com> wrote:
> Hi,
>
> Try issue command " make clean", then configure and make.
> This works for me.
>
> Terry
>
>
> On Thu, Jan 19, 2012 at 7:46 PM, Per Jr. Greisen <pgreisen.gmail.com> wrote:
>
>> Hi
>>
>> I am trying to install amber10 but it terminates with the following error
>>
>> ./configure_amber -gfortran in amber10/src/
>> make serial
>>
>> make[2]: Leaving directory `/xbar/nas1/home3/riso/mgrub/amber10/src/dcqtp'
>> gfortran -ffree-form -o sander constants.o nose_hoover.o
>> nose_hoover_vars.o nose_hoover_init.o stack.o qmmm_module.o
>> qm2_dftb_module.o trace.o lmod.o decomp.o icosasurf.o egb.o remd.o
>> findmask.o pb_force.o pb_exmol.o pb_mpfrc.o pb_direct.o pb_list.o
>> np_force.o sa_driver.o relax_mat.o nmr.o multisander.o sander.o
>> trajene.o cshf.o nmrcal.o pearsn.o printe.o runmin.o rdparm.o mdread.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.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
>> random.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 veclib.o is_init.o
>> constantph.o prn_dipoles.o ips.o sglds.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 spatial_recip.o
>> spatial_fft.o parms.o softcore.o molecule.o xref.o dssp.o qm_mm.o
>> qm_link_atoms.o qm_ewald.o qm_gb.o qm_zero_charges.o qm_print_info.o
>> qm_assign_atom_types.o qm2_allocate_e_repul.o qm2_calc_charges.o
>> qm2_calc_rij_and_eqns.o qm2_dihed.o qm2_energy.o qm2_fock.o
>> qm2_get_qm_forces.o qm2_get_qmmm_forces.o qm2_h1elec.o
>> qm2_hcore_qmqm.o qm2_hcore_qmmm.o qm2_identify_peptide_links.o
>> qm2_load_params_and_allocate.o qm2_repp.o qm2_rotate_qmqm.o qm2_scf.o
>> qm2_setup_orb_exp.o qm2_smallest_number.o qm2_dftb_broyden.o
>> qm2_dftb_dispersion_egr.o qm2_dftb_dispersion_params.o
>> qm2_dftb_dispersionread.o qm2_dftb_scf.o qm2_dftb_energy.o
>> qm2_dftb_ewevge.o qm2_dftb_externalshift.o qm2_dftb_fermi.o
>> qm2_dftb_get_qm_forces.o qm2_dftb_gamma.o qm2_dftb_gammamat.o
>> qm2_dftb_get_qmmm_forces.o qm2_dftb_gettab.o qm2_dftb_load_params.o
>> qm2_dftb_mulliken.o qm2_dftb_repulsiv.o qm2_dftb_self.o
>> qm2_dftb_shift.o qm2_dftb_short_range.o qm2_dftb_skpar.o
>> qm2_dftb_slkode.o qm2_dftb_slktrafo.o qm2_dftb_read_cm3.o
>> qm2_dftb_cm3.o qm2_dftb_ewald.o qm2_dftb_gb.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 qm_div.o force.o \
>> ../lmod/lmod.a ../dcqtp/src/qmmm/libdivcon.a mt19937.o
>> ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o
>> ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-utils.o
>> ncsu-colvar.o ncsu-constants.o ncsu-cv-ANGLE.o ncsu-cv-DISTANCE.o
>> ncsu-cv-HANDEDNESS.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-smd-hooks.o
>> ncsu-umbrella.o ncsu-utils.o ncsu-value.o \
>> ../lapack/lapack.a ../blas/blas.a \
>> ../lib/nxtsec.o ../lib/sys.a ../netcdf/lib/libnetcdf.a
>> ../lmod/lmod.a(dsaupd.o): In function `dsaupd_':
>> _dsaupd.f:(.text+0x29d): undefined reference to `ambsecond_'
>> _dsaupd.f:(.text+0x4df): undefined reference to `ambsecond_'
>> ../lmod/lmod.a(dsaup2.o): In function `dsaup2_':
>> _dsaup2.f:(.text+0x147): undefined reference to `ambsecond_'
>> _dsaup2.f:(.text+0x338): undefined reference to `ambsecond_'
>> _dsaup2.f:(.text+0x4a2): undefined reference to `ambsecond_'
>> ../lmod/lmod.a(dsaup2.o):_dsaup2.f:(.text+0x6b0): more undefined
>> references to `ambsecond_' follow
>> collect2: ld returned 1 exit status
>> make[1]: *** [sander] Error 1
>> make[1]: Leaving directory `/xbar/nas1/home3/riso/mgrub/amber10/src/sander'
>> make: *** [serial] Error 2
>> ~/amber10/src
>>
>> How to resolve this thanks
>>
>> --
>> Per
>>
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>>
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--
Per
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Received on Thu Jan 19 2012 - 06:00:03 PST
