Re: [AMBER] problems compiling ambertool

From: Per Jr. Greisen <>
Date: Wed, 18 Mar 2009 11:49:57 +0000

Hi all,

There are still a lot of problem compiling amber on Sun but looking at the
makefile there are not that many directories missing in order to get an
executable(I hope) - but there seem to be a problem for get the libnetcdf.a
correctly linked into sander

cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
f90 -free -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 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 -lm
Undefined first referenced
 symbol in file
qm_mm_div_ qm_div.o
ld: fatal: Symbol referencing errors. No output written to sander
*** Error code 1
make: Fatal error: Command failed for target `sander'
Current working directory

On Tue, Mar 17, 2009 at 6:24 PM, Bill Ross <> wrote:

> > write(gnIout,*) 'External radii file found& !!', &
> Possibly the "!!" is treated like a comment-starter, thus hiding the
> second single-quote.
> Bill
> _______________________________________________
> AMBER mailing list
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Received on Fri Mar 20 2009 - 01:08:16 PDT
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