cd /share/apps/Amber/amber16/AmberTools/src && make install make[1]: Entering directory '/share/apps/Amber/amber16/AmberTools/src' Starting installation of AmberTools17 serial at Tue Jul 31 21:32:45 +0430 2018. (cd ucpp-1.3 && make install ) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/ucpp-1.3' gcc -o ucpp mem.o nhash.o cpp.o lexer.o assert.o macro.o eval.o mv ucpp /share/apps/Amber/amber16//bin make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/ucpp-1.3' (cd byacc && make install ) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/byacc' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/byacc' (cd arpack && make install ); make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/arpack' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/arpack' (cd lapack && make install ) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lapack' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lapack' (cd blas && make install ) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/blas' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/blas' (cd c9x-complex && make skip ) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/c9x-complex' using built-in (C99) complex.h functionality make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/c9x-complex' (cd pbsa && make install ) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/pbsa' gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o decomp.o decomp.F90 Always rebuild [ pb_lsolver.o [ cuda_cg_wrapper.o band2csr.o ]] to make predefined macros effective gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pb_lsolver.o pb_lsolver.F90 cd ../lib && make nxtsec.o random.o cd ../lapack && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lib' make[3]: 'nxtsec.o' is up to date. make[3]: 'random.o' is up to date. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lib' make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lapack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lapack' cd ../blas && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/blas' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/blas' cd ../arpack && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/arpack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/arpack' gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pbsa.o pbsa.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pb_force.o pb_force.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o np_force.o np_force.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pb_write.o pb_write.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pb_fdfrc.o pb_fdfrc.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pb_crgview.o pb_crgview.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pb_bldsys.o pb_bldsys.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pb_direct.o pb_direct.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pb_list.o pb_list.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o problem.o problem.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pb_chkfrc.o pb_chkfrc.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o rdpqr.o rdpqr.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pb_read.o pb_read.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o force.o force.F90 gfortran -DBINTRAJ -DEMIL -c -O0 -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pb_init.o pb_init.F90 gfortran -DBINTRAJ -DEMIL -c -O3 -mtune=native -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pb_fddrv.o pb_fddrv.F90 gfortran -DBINTRAJ -DEMIL -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o pbsa dsvdc.o pbsa.o pb_read.o pb_write.o getcoor.o runmd.o runmin.o force.o pbsa_lib.o pb_init.o sa_driver.o density.o np_force.o pb_force.o pb_p3m.o pb_fdfrc.o pb_crgview.o pb_fddrv.o pb_iimdrv.o pb_nlsolver.o pb_bldsys.o pb_mpfrc.o pb_direct.o pb_list.o timer.o egb.o ene.o locmem.o myopen.o rdparm.o pb_lsolver.o decomp.o rgroup.o rfree.o debug.o coed20.o irre32.o phidev.o project.o qld.o coed6.o irre31.o miniop.o iimod.o prodis.o qint.o wint.o transf.o curv.o GrToPr.o jumps.o problem.o regular.o gmres.o daxpy.o ddot.o dheqr.o dpigmr.o dscal.o dslui2.o dxlcal.o dchkw.o dgmres.o dnrm2.o drlcal.o dsilus.o dslui.o isdgmr.o dcopy.o dhels.o dorth.o ds2y.o dslugm.o dsmv.o qs2i1d.o d1mach.o fdump.o i1mach.o j4save.o xercnt.o xerhlt.o xermsg.o xerprn.o xersve.o xgetua.o bicg.o dbcg.o dslui4.o dsluti.o dsmtv.o dslubc.o isdbcg.o pb_chkfrc.o svdcmp.o svbksb.o pythag.o pb_augdrv.o gmresX.o interpX.o matvec3.o gen_dx_file.o aug_iccg.o parms.o memory_module.o rdpqr.o \ ../lib/nxtsec.o ../lib/random.o \ -L/share/apps/Amber/amber16//lib -larpack -llapack -lblas -lxblas-amb /bin/mv pbsa /share/apps/Amber/amber16//bin make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/pbsa' (cd gbnsr6 && make install ) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/gbnsr6' cd ../lib && make nxtsec.o random.o cd ../lapack && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lib' make[3]: 'nxtsec.o' is up to date. make[3]: 'random.o' is up to date. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lib' make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lapack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lapack' cd ../blas && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/blas' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/blas' cd ../arpack && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/arpack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/arpack' gfortran -DBINTRAJ -DEMIL -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o gbnsr6 gbnsr6.o pb_read.o gb_read.o pb_write.o getcoor.o runmd.o runmin.o force.o pb_init.o sa_driver.o np_force.o variable_module.o pb_exmol.o NSR6routines.o pb_list.o timer.o egb.o ene.o locmem.o myopen.o rdparm.o decomp.o rgroup.o rfree.o debug.o svdcmp.o svbksb.o parms.o pythag.o memory_module.o gen_dx_file.o \ ../lib/nxtsec.o ../lib/random.o \ -L/share/apps/Amber/amber16//lib -larpack -llapack -lblas -lxblas-amb /bin/mv gbnsr6 /share/apps/Amber/amber16//bin make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/gbnsr6' (cd cifparse && make install ) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/cifparse' /bin/rm -f libcifparse.a ar rv libcifparse.a lex.cif.o cifp.tab.o cifparse.o ar: creating libcifparse.a a - lex.cif.o a - cifp.tab.o a - cifparse.o ranlib libcifparse.a mv libcifparse.a /share/apps/Amber/amber16//lib make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/cifparse' (cd antechamber && make install ) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/antechamber' gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN acdoctor.o eprintf.o \ -L/share/apps/Amber/amber16//lib -lcifparse -lm -o acdoctor gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN antechamber.o eprintf.o \ -L/share/apps/Amber/amber16//lib -lcifparse -lm -o antechamber SFX= BINDIR=/share/apps/Amber/amber16//bin sh patch.sh cp acdoctor /share/apps/Amber/amber16//bin/to_be_dispatched/acdoctor cp antechamber /share/apps/Amber/amber16//bin/to_be_dispatched/antechamber make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/antechamber' (cd sqm && make install ) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/sqm' cd ../lapack; make install cd ../lib; make sys.a make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lib' make[3]: 'sys.a' is up to date. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lib' make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lapack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lapack' cd ../blas; make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/blas' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/blas' cd ../arpack && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/arpack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/arpack' gfortran -DBINTRAJ -DEMIL -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o sqm file_io_dat.o constants.o findmask.o sqm.SQM.o xmin.o xminC.o amopen.o mexit.o assert.o timer_dummy.o nmlsrc.o qm_print_info.SQM.o qm2_energy.SQM.o qm2_read_nm_and_alloc.SQM.o qm2_scf.SQM.o qm2_dftb_scf.SQM.o qm2_allocate_e_repul.o qm2_calc_charges.o qm2_calc_dipole.o qm2_calc_rij_and_eqns.o qm2_dihed.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_core_core_repulsion.o qm2_core_core_repulsion_dxyz.o qm2_iterator_mod.o qm2_diagonalizer_module.o qm2_setup_orb_exp.o qm2_smallest_number.o qm2_fock_predict.o qm_gb.o qm_zero_charges.o qm_assign_atom_types.o qm_link_atoms.o qm2_print_charges.o qmmm_qmtheorymodule.o qm2_print_bondorders.o qm2_pm6_hof_module.o qm2_params_module.o qm2_dftb_module.o qm2_dftb_broyden.o qm2_dftb_dispersion_egr.o qm2_dftb_dispersion_params.o qm2_dftb_dispersionread.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_skpar.o qm2_dftb_slkode.o qm2_dftb_slktrafo.o qm2_dftb_read_cm3.o qm2_dftb_cm3.o qm2_dftb_gb.o qm2_dftb_3rd_order.o qmmm_module.o qmmm_nml_module.o qmmm_struct_module.o qmmm_vsolv_module.o qm2_parameters.o dh_correction_module.o utilitiesModule.o elementOrbitalIndex.o parameterReader.o slater_overlap.o qm2_h1elec_d.o rotation.o qm2_repp_d.o opnq_Edisp.o opnq_Erep.o opnq_Evdw.o opnq.o opnq_SwitchMod.o qm2_fock_d.o MNDOChargeSeparation.o qm2_print_energy.o qm2_dftb_get_dftb3_parameters.o qm2_dftb_gamma_dftb3.o \ -L/share/apps/Amber/amber16//lib -larpack -llapack -lblas -lxblas-amb ../lib/sys.a mv sqm /share/apps/Amber/amber16//bin make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/sqm' (cd reduce && make install ) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/reduce' installing ./toolclasses... make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/reduce/toolclasses' make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/reduce/toolclasses' installing ./libpdb... make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/reduce/libpdb' make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/reduce/libpdb' installing ./reduce_src... make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/reduce/reduce_src' g++ -o reduce GraphToHoldScores.o reduce.o CTab.o ElementInfo.o StdResH.o ResBlk.o AtomConn.o AtomPositions.o DotSph.o Mover.o RotMethyl.o RotAromMethyl.o RotDonor.o FlipMemo.o CliqueList.o AtomDescr.o PDBrec.o MoveableNode.o hybrid_36_c.o -L../libpdb -lpdb++ -L../toolclasses -ltoolclasses -lm mv reduce /share/apps/Amber/amber16//bin/to_be_dispatched/ cat ../reduce_template | sed "s/REPLACE_ME/reduce/" > /share/apps/Amber/amber16//bin/reduce chmod +x /share/apps/Amber/amber16//bin/reduce /bin/rm -f /share/apps/Amber/amber16//dat/reduce_wwPDB_het_dict.txt cp /share/apps/Amber/amber16/AmberTools/src/reduce/reduce_wwPDB_het_dict.txt /share/apps/Amber/amber16//dat/reduce_wwPDB_het_dict.txt make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/reduce/reduce_src' make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/reduce' (cd leap && make install ) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/leap' Compiling basic programs cd src/leap && make installteLeap make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/leap/src/leap' gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN \ -o teLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o collection.o container.o internal.o list.o loop.o molecule.o oDouble.o oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o graphUtil.o select.o amber.o build.o elements.o library.o chirality.o minimizer.o model.o parmLib.o pdbFile.o mol2File.o mol3File.o tools.o variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o restraint.o hybrid.o tLeap.o -lm /share/apps/Amber/amber16//lib/libnetcdf.a mv teLeap /share/apps/Amber/amber16//bin make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/leap/src/leap' Copying shell script cp tleap /share/apps/Amber/amber16//bin/tleap chmod +x /share/apps/Amber/amber16//bin/tleap make skip_xleap make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/leap' NOTE: skipping the building of xleap as X11 libraries are not installed or NOTE: -nox11 was specified as an option to configure. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/leap' make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/leap' (cd lib && make install) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lib' gfortran -DBINTRAJ -DEMIL -fPIC -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o new2oldparm new2oldparm.o \ nxtsec.o mv new2oldparm /share/apps/Amber/amber16//bin /bin/rm -f make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lib' (cd addles && make install) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/addles' cd ../lib && make mexit.o nxtsec.o make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lib' make[3]: 'mexit.o' is up to date. make[3]: 'nxtsec.o' is up to date. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lib' gfortran -DBINTRAJ -DEMIL -fPIC -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include \ -o /share/apps/Amber/amber16//bin/addles lesmain.o addspace.o readprm.o writprm.o readcrd.o writcrd.o pick.o rline.o nxt.o intgr.o find.o of.o geti.o unit.o getc.o alert.o echo.o get4c.o getd.o wlesprm.o lesprm.o random.o les2prm.o checksz.o addspace_atm1st.o \ ../lib/mexit.o ../lib/nxtsec.o make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/addles' (cd sander && make serial) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/sander' cd ../sqm && make libsqm make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/sqm' make[3]: Nothing to be done for 'libsqm'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/sqm' test -e qmmm_module.o || touch qmmm_module.o /bin/rm -f ../pbsa/decomp.o ../pbsa/decomp.mod ../pbsa/decomp.MOD /bin/cp -p decomp.o decomp.mod ../pbsa cd ../pbsa && make libFpbsa.a make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/pbsa' ar rv libFpbsa.a interpX.SANDER.o np_force.SANDER.o pb_fdfrc.SANDER.o pb_force.SANDER.o pb_init.SANDER.o pb_p3m.SANDER.o pb_read.SANDER.o pb_write.SANDER.o sa_driver.SANDER.o timer.SANDER.o curv.SANDER.o density.SANDER.o dsvdc.SANDER.o gen_dx_file.SANDER.o GrToPr.SANDER.o iimod.SANDER.o memory_module.SANDER.o miniop.SANDER.o pb_bldsys.SANDER.o pb_crgview.SANDER.o pb_direct.SANDER.o pb_fddrv.SANDER.o pb_list.SANDER.o pb_lsolver.SANDER.o pb_mpfrc.SANDER.o pb_nlsolver.SANDER.o pbsa_lib.SANDER.o phidev.SANDER.o project.SANDER.o pythag.SANDER.o svbksb.SANDER.o svdcmp.SANDER.o transf.SANDER.o ar: creating libFpbsa.a a - interpX.SANDER.o a - np_force.SANDER.o a - pb_fdfrc.SANDER.o a - pb_force.SANDER.o a - pb_init.SANDER.o a - pb_p3m.SANDER.o a - pb_read.SANDER.o a - pb_write.SANDER.o a - sa_driver.SANDER.o a - timer.SANDER.o a - curv.SANDER.o a - density.SANDER.o a - dsvdc.SANDER.o a - gen_dx_file.SANDER.o a - GrToPr.SANDER.o a - iimod.SANDER.o a - memory_module.SANDER.o a - miniop.SANDER.o a - pb_bldsys.SANDER.o a - pb_crgview.SANDER.o a - pb_direct.SANDER.o a - pb_fddrv.SANDER.o a - pb_list.SANDER.o a - pb_lsolver.SANDER.o a - pb_mpfrc.SANDER.o a - pb_nlsolver.SANDER.o a - pbsa_lib.SANDER.o a - phidev.SANDER.o a - project.SANDER.o a - pythag.SANDER.o a - svbksb.SANDER.o a - svdcmp.SANDER.o a - transf.SANDER.o ranlib libFpbsa.a /bin/mv libFpbsa.a /share/apps/Amber/amber16//lib make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/pbsa' /bin/rm -f ../pbsa/decomp.o ../pbsa/decomp.mod ../pbsa/decomp.MOD test -e poisson_boltzmann.o || touch poisson_boltzmann.o test -e qm2_read_nm_and_alloc.o || touch qm2_read_nm_and_alloc.o test -e qmmm_vsolv_module.o || touch qmmm_vsolv_module.o test -e elementOrbitalIndex.o || touch elementOrbitalIndex.o test -e utilitiesmodule.o || touch utilitiesmodule.o test -e qmmm_nml_module.o || touch qmmm_nml_module.o test -e qmmm_struct_module.o || touch qmmm_struct_module.o make -C ../emil install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/emil' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/emil' cd ../sebomd && make sebomd.a make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/sebomd' make[3]: 'sebomd.a' is up to date. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/sebomd' test -e dispersion_cavity.o || touch dispersion_cavity.o test -e pbtimer_module.o || touch pbtimer_module.o cd ../lib && make sys.a make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lib' make[3]: 'sys.a' is up to date. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lib' cd ../blas && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/blas' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/blas' cd ../lapack && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lapack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lapack' cd ../arpack && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/arpack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/arpack' if [ -n "-DRISMSANDER" ]; then \ cd ../rism && make librism; \ fi make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/rism' ar rv /share/apps/Amber/amber16//lib/librism.a rism1d_c.o solvmdl_c.o rism1d_potential_c.o rism1d_closure_c.o rism1d_kh_c.o rism1d_hnc_c.o rism1d_py_c.o rism1d_mv0_c.o rism1d_psen_c.o rism1d_nub_c.o rism1d_polyt_c.o rism1d_devb_c.o quaternion.o array_util.o rism_util.o rism_report_c.o rism3d_grid_c.o rism3d_closure_c.o rism3d_kh_c.o rism3d_hnc_c.o rism3d_psen_c.o rism3d_c.o rism3d_potential_c.o rism3d_restart.o rism3d_xyzv.o rism3d_opendx.o rism3d_ccp4.o rism3d_solvent_c.o rism3d_solute_c.o pubfft.o rism3d_fft.o rism_parm.o rism_io.o mdiis_orig_c.o mdiis_blas_c.o mdiis_blas2_c.o mdiis_c.o fce_c.o erfcfun.o safemem.o blend.o rism_timer_c.o constants.o getopts_c.o bspline.o fftw3.o r - rism1d_c.o r - solvmdl_c.o r - rism1d_potential_c.o r - rism1d_closure_c.o r - rism1d_kh_c.o r - rism1d_hnc_c.o r - rism1d_py_c.o r - rism1d_mv0_c.o r - rism1d_psen_c.o r - rism1d_nub_c.o r - rism1d_polyt_c.o r - rism1d_devb_c.o r - quaternion.o r - array_util.o r - rism_util.o r - rism_report_c.o r - rism3d_grid_c.o r - rism3d_closure_c.o r - rism3d_kh_c.o r - rism3d_hnc_c.o r - rism3d_psen_c.o r - rism3d_c.o r - rism3d_potential_c.o r - rism3d_restart.o r - rism3d_xyzv.o r - rism3d_opendx.o r - rism3d_ccp4.o r - rism3d_solvent_c.o r - rism3d_solute_c.o r - pubfft.o r - rism3d_fft.o r - rism_parm.o r - rism_io.o r - mdiis_orig_c.o r - mdiis_blas_c.o r - mdiis_blas2_c.o r - mdiis_c.o r - fce_c.o r - erfcfun.o r - safemem.o r - blend.o r - rism_timer_c.o r - constants.o r - getopts_c.o r - bspline.o r - fftw3.o ranlib /share/apps/Amber/amber16//lib/librism.a make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/rism' gfortran -DBINTRAJ -DEMIL -fPIC -ffree-form -I../pbsa -I../sqm -I../rism -I../../../include -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o /share/apps/Amber/amber16//bin/sander file_io_dat.o constants.o state.o memory_module.o stack.o nose_hoover.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.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o printe.o runmin.o rdparm.o sander_lib.o mdread.o locmem.o runmd.o relaxmd.o quench.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 pol_gauss.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_bndpol.o ew_dipole_recip.o mexit.o new_time.o extra_pts.o thermo_int.o matinv.o assert.o erfcfun.o sinr_t.o constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.o emil.o mdin_emil_dat.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 ../rism/amber_rism_interface.SANDER.o AmberNetcdf.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 amd.o scaledMD.o barostats.o random.o les.o abfqmmm_module.o qm_mm.o qm_ewald.o qmmm_vsolv.o qm2_extern_util_module.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 qm2_extern_qc_module.o qm2_extern_mrcc_module.o qm2_extern_genmpi_module.o qmmm_adaptive_module.o prn_qmmm_dipole.o sebomd_module.o sebomd_arrays.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.o -L/share/apps/Amber/amber16//lib -lsqm \ nfe-abmd-hooks.o nfe-bbmd-ctxt.o nfe-bbmd-hooks.o nfe-colvar.o nfe-colvar-math.o nfe-colvar-type.o nfe-colvar-utils.o nfe-constants.o nfe-cv-ANGLE.o nfe-cv-COM_ANGLE.o nfe-cv-COM_DISTANCE.o nfe-cv-COM_TORSION.o nfe-cv-COS_OF_DIHEDRAL.o nfe-cv-DISTANCE.o nfe-cv-HANDEDNESS.o nfe-cv-LCOD.o nfe-cv-MULTI_RMSD.o nfe-cv-N_OF_BONDS.o nfe-cv-N_OF_STRUCTURES.o nfe-cv-R_OF_GYRATION.o nfe-cv-TORSION.o nfe-pmd-hooks.o nfe-rmsd.o nfe-sander-hooks.o nfe-sander-proxy.o nfe-stsm-hooks.o nfe-cv-PCA.o nfe-read-pca.o nfe-cv-SIN_OF_DIHEDRAL.o nfe-cv-PAIR_DIHEDRAL.o nfe-cv-PATTERN_DIHEDRAL.o nfe-cv-DF_COM_DISTANCE.o nfe-smd-hooks.o nfe-umbrella.o nfe-utils.o nfe-value.o mt19937.o xray_fourier.o xray_globals.o xray_interface.o xray_real_space.o xray_reciprocal_space.o xray_utils.o \ -lFpbsa ../lib/nxtsec.o /share/apps/Amber/amber16//lib/libemil.a -lstdc++ \ ../sebomd/sebomd.a \ ../lib/sys.a /share/apps/Amber/amber16//lib/libnetcdff.a /share/apps/Amber/amber16//lib/libnetcdf.a \ -lrism /share/apps/Amber/amber16//lib/libfftw3.a -larpack -llapack -lblas -lxblas-amb \ Plumed.o -ldl -Wl,-export-dynamic gfortran -DBINTRAJ -DEMIL -fPIC -ffree-form -I../pbsa -I../sqm -I../rism -I../../../include -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o /share/apps/Amber/amber16//bin/sander.LES memory_module.o stack.o file_io_dat.o constants.o state.o nose_hoover.o nose_hoover_init_LES.o trace.o rmsgrd.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o egb.LES.o remd.LES.o findmask.o relax_mat.o nmr.LES.o multitmd.o multisander.LES.o sander.LES.o cshf.o nmrcal.o mtmdcall.o pearsn.o printe.o runmin.o nonbond_list.LES.o force.LES.o rdparm.LES.o mdread.LES.o locmem.LES.o runmd.LES.o relaxmd.o quench.o degcnt.LES.o decnvh.o fastwt.o parallel.LES.o shake.o ene.LES.o dynlib.LES.o nmlsrc.o ew_force.LES.o ew_setup.LES.o ew_bspline.o ew_fft.o short_ene.LES.o pol_gauss.o ew_recip.LES.o pcshift.o align.o csa.o rfree.o rgroup.o amopen.o sander_lib.o random.o debug.o ew_recip_reg.o ew_handle_dips.o ew_bndpol.o ew_dipole_recip.o mexit.o new_time.o extra_pts.LES.o thermo_int.o matinv.o assert.o erfcfun.o sinr_t.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 emil.o mdin_emil_dat.o ../rism/amber_rism_interface.SANDER.o sebomd_module.o sebomd_arrays.o les.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 barostats.o qm_ewald.o qmmm_vsolv.o qm2_extern_util_module.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 qm2_extern_qc_module.o qm2_extern_mrcc_module.o qm2_extern_genmpi_module.o qmmm_adaptive_module.o abfqmmm_module.o prn_qmmm_dipole.o AmberNetcdf.o bintraj.LES.o binrestart.LES.o getcor.LES.o mdfil.LES.o mdwrit.LES.o lmod.LES.o trajene.o ew_box.LES.o minrit.LES.o set.LES.o qm_mm.LES.o amd.o scaledMD.o pimd_vars.o pimd_force.LES.o pimd_init.LES.o cmd_vars.o cmd_matrix.LES.o lscivr_vars.o lsc_init.o lsc_xp.o \ xray_fourier.o xray_globals.o xray_interface.o xray_real_space.o xray_reciprocal_space.o xray_utils.o -L/share/apps/Amber/amber16//lib -lsqm -lFpbsa /share/apps/Amber/amber16//lib/libemil.a -lstdc++ \ ../sebomd/sebomd.a \ ../lib/nxtsec.o ../lib/sys.a nfe-abmd-hooks.o nfe-bbmd-ctxt.o nfe-bbmd-hooks.o nfe-colvar.o nfe-colvar-math.o nfe-colvar-type.o nfe-colvar-utils.o nfe-constants.o nfe-cv-ANGLE.o nfe-cv-COM_ANGLE.o nfe-cv-COM_DISTANCE.o nfe-cv-COM_TORSION.o nfe-cv-COS_OF_DIHEDRAL.o nfe-cv-DISTANCE.o nfe-cv-HANDEDNESS.o nfe-cv-LCOD.o nfe-cv-MULTI_RMSD.o nfe-cv-N_OF_BONDS.o nfe-cv-N_OF_STRUCTURES.o nfe-cv-R_OF_GYRATION.o nfe-cv-TORSION.o nfe-pmd-hooks.o nfe-rmsd.o nfe-sander-hooks.o nfe-sander-proxy.o nfe-stsm-hooks.o nfe-cv-PCA.o nfe-read-pca.o nfe-cv-SIN_OF_DIHEDRAL.o nfe-cv-PAIR_DIHEDRAL.o nfe-cv-PATTERN_DIHEDRAL.o nfe-cv-DF_COM_DISTANCE.o nfe-smd-hooks.o nfe-umbrella.o nfe-utils.o nfe-value.o mt19937.o /share/apps/Amber/amber16//lib/libnetcdff.a /share/apps/Amber/amber16//lib/libnetcdf.a \ -lrism /share/apps/Amber/amber16//lib/libfftw3.a -larpack -llapack -lblas -lxblas-amb \ Plumed.o -ldl -Wl,-export-dynamic gfortran -shared -DBINTRAJ -DEMIL -fPIC -ffree-form -I../pbsa -I../sqm -I../rism -I../../../include -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o /share/apps/Amber/amber16//lib/libsander.so file_io_dat.o constants.o state.o memory_module.o stack.o nose_hoover.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 trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o printe.o runmin.o rdparm.API.o cpparm.o sander_lib.o mdread.o locmem.o runmd.o relaxmd.o quench.o getcor.o degcnt.o decnvh.o fastwt.API.o parallel.o shake.o ene.o mdwrit.o minrit.o set.API.o dynlib.API.o mdfil.o nmlsrc.o ew_force.o ew_setup.API.o ew_box.API.o ew_bspline.o ew_fft.o nonbond_list.API.o short_ene.o pol_gauss.o ew_recip.o pcshift.o align.o csa.o rfree.o rgroup.o amopen.o debug.API.o ew_recip_reg.o ew_handle_dips.o ew_bndpol.o ew_dipole_recip.o mexit.o new_time.API.o extra_pts.API.o thermo_int.o les.o matinv.o assert.o erfcfun.o sinr_t.o constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.o emil.o mdin_emil_dat.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 ../rism/amber_rism_interface.SANDER.o AmberNetcdf.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.API.o crg_reloc.o amd.o scaledMD.o barostats.o interface.o random.o qm_mm.API.o prmtop_type.o \ abfqmmm_module.o qm_ewald.o qmmm_vsolv.o qm2_extern_util_module.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 qm2_extern_qc_module.o qm2_extern_mrcc_module.o qm2_extern_genmpi_module.o qmmm_adaptive_module.o prn_qmmm_dipole.o sebomd_module.o sebomd_arrays.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.o \ -L/share/apps/Amber/amber16//lib -lsqm \ nfe-abmd-hooks.o nfe-bbmd-ctxt.o nfe-bbmd-hooks.o nfe-colvar.o nfe-colvar-math.o nfe-colvar-type.o nfe-colvar-utils.o nfe-constants.o nfe-cv-ANGLE.o nfe-cv-COM_ANGLE.o nfe-cv-COM_DISTANCE.o nfe-cv-COM_TORSION.o nfe-cv-COS_OF_DIHEDRAL.o nfe-cv-DISTANCE.o nfe-cv-HANDEDNESS.o nfe-cv-LCOD.o nfe-cv-MULTI_RMSD.o nfe-cv-N_OF_BONDS.o nfe-cv-N_OF_STRUCTURES.o nfe-cv-R_OF_GYRATION.o nfe-cv-TORSION.o nfe-pmd-hooks.o nfe-rmsd.o nfe-sander-hooks.o nfe-sander-proxy.o nfe-stsm-hooks.o nfe-cv-PCA.o nfe-read-pca.o nfe-cv-SIN_OF_DIHEDRAL.o nfe-cv-PAIR_DIHEDRAL.o nfe-cv-PATTERN_DIHEDRAL.o nfe-cv-DF_COM_DISTANCE.o nfe-smd-hooks.o nfe-umbrella.o nfe-utils.o nfe-value.o mt19937.o xray_fourier.o xray_globals.o xray_interface.o xray_real_space.o xray_reciprocal_space.o xray_utils.o \ -lFpbsa ../lib/nxtsec.o /share/apps/Amber/amber16//lib/libemil.a -lstdc++ \ ../sebomd/sebomd.a \ ../lib/sys.a /share/apps/Amber/amber16//lib/libnetcdff.a /share/apps/Amber/amber16//lib/libnetcdf.a \ -lrism fftw3_dummy.o -larpack -llapack -lblas -lxblas-amb \ Plumed.o -ldl -Wl,-export-dynamic gfortran -shared -DBINTRAJ -DEMIL -fPIC -ffree-form -I../pbsa -I../sqm -I../rism -I../../../include -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include \ -o /share/apps/Amber/amber16//lib/libsanderles.so memory_module.o stack.o file_io_dat.o les.o constants.o state.o nose_hoover.o nose_hoover_init_LES.o trace.o rmsgrd.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o egb.LES.o remd.LES.o findmask.o relax_mat.o nmr.LES.o multitmd.o cshf.o nmrcal.o mtmdcall.o pearsn.o cpparm.LES.o printe.o runmin.o nonbond_list.LESAPI.o force.LES.o rdparm.LESAPI.o mdread.LES.o locmem.LES.o runmd.LES.o relaxmd.o quench.o degcnt.LES.o decnvh.o fastwt.API.o parallel.LES.o shake.o ene.LES.o dynlib.LESAPI.o nmlsrc.o ew_force.LES.o ew_setup.LESAPI.o ew_bspline.o ew_fft.o short_ene.LES.o pol_gauss.o ew_recip.LES.o pcshift.o align.o csa.o rfree.o rgroup.o amopen.o sander_lib.o random.o debug.API.o ew_recip_reg.o ew_handle_dips.o ew_bndpol.o ew_dipole_recip.o mexit.o new_time.API.o extra_pts.LESAPI.o thermo_int.o matinv.o assert.o erfcfun.o sinr_t.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 emil.o mdin_emil_dat.o ../rism/amber_rism_interface.SANDER.o sebomd_module.o sebomd_arrays.o spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o linear_response.o molecule.o xref.o dssp.o charmm.API.o crg_reloc.o barostats.o prmtop_type.o AmberNetcdf.o bintraj.LES.o binrestart.LES.o getcor.LES.o mdfil.LES.o mdwrit.LES.o lmod.LES.o trajene.o ew_box.LESAPI.o minrit.LES.o set.LESAPI.o qm_mm.LESAPI.o amd.o scaledMD.o interface.LESAPI.o abfqmmm_module.o qm_ewald.o qmmm_vsolv.o qm2_extern_util_module.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 qm2_extern_qc_module.o qm2_extern_mrcc_module.o qm2_extern_genmpi_module.o qmmm_adaptive_module.o prn_qmmm_dipole.o pimd_vars.o pimd_force.LES.o pimd_init.LES.o cmd_vars.o cmd_matrix.LES.o lscivr_vars.o lsc_init.o lsc_xp.o \ xray_fourier.o xray_globals.o xray_interface.o xray_real_space.o xray_reciprocal_space.o xray_utils.o -L/share/apps/Amber/amber16//lib -lsqm -lFpbsa /share/apps/Amber/amber16//lib/libemil.a -lstdc++ \ ../sebomd/sebomd.a Plumed.o -ldl -Wl,-export-dynamic \ ../lib/nxtsec.o ../lib/sys.a nfe-abmd-hooks.o nfe-bbmd-ctxt.o nfe-bbmd-hooks.o nfe-colvar.o nfe-colvar-math.o nfe-colvar-type.o nfe-colvar-utils.o nfe-constants.o nfe-cv-ANGLE.o nfe-cv-COM_ANGLE.o nfe-cv-COM_DISTANCE.o nfe-cv-COM_TORSION.o nfe-cv-COS_OF_DIHEDRAL.o nfe-cv-DISTANCE.o nfe-cv-HANDEDNESS.o nfe-cv-LCOD.o nfe-cv-MULTI_RMSD.o nfe-cv-N_OF_BONDS.o nfe-cv-N_OF_STRUCTURES.o nfe-cv-R_OF_GYRATION.o nfe-cv-TORSION.o nfe-pmd-hooks.o nfe-rmsd.o nfe-sander-hooks.o nfe-sander-proxy.o nfe-stsm-hooks.o nfe-cv-PCA.o nfe-read-pca.o nfe-cv-SIN_OF_DIHEDRAL.o nfe-cv-PAIR_DIHEDRAL.o nfe-cv-PATTERN_DIHEDRAL.o nfe-cv-DF_COM_DISTANCE.o nfe-smd-hooks.o nfe-umbrella.o nfe-utils.o nfe-value.o mt19937.o /share/apps/Amber/amber16//lib/libnetcdff.a /share/apps/Amber/amber16//lib/libnetcdf.a \ -lrism fftw3_dummy.o -larpack -llapack -lblas -lxblas-amb make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/sander' (cd nmr_aux && make install) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/nmr_aux' cd prepare_input && make clean && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/nmr_aux/prepare_input' /bin/rm -f *.o make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/nmr_aux/prepare_input' make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/nmr_aux/prepare_input' gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -o makeDIST_RST.o makeDIST_RST.c gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -o makeANG_RST.o makeANG_RST.c gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -o nef_to_RST.o nef_to_RST.c gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -o makeANG_RST makeANG_RST.o \ -lm gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -o makeDIST_RST makeDIST_RST.o \ -lm gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -o nef_to_RST nef_to_RST.o \ -lm -L/share/apps/Amber/amber16//lib -lcifparse mv makeDIST_RST makeANG_RST nef_to_RST /share/apps/Amber/amber16//bin cp makeCHIR_RST /share/apps/Amber/amber16//bin cp map.NEF-AMBER map.DG-AMBER /share/apps/Amber/amber16//dat make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/nmr_aux/prepare_input' cd fantasian && make clean && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/nmr_aux/fantasian' /bin/rm -f *.o fantasian make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/nmr_aux/fantasian' make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/nmr_aux/fantasian' gfortran -DBINTRAJ -DEMIL -c -O0 -fPIC -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o fantasian.o fantasian.F gfortran -DBINTRAJ -DEMIL -fPIC -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o fantasian fantasian.o ../../lib/random.o ../../lib/mexit.o mv fantasian /share/apps/Amber/amber16//bin make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/nmr_aux/fantasian' cp senergy sviol sviol2 /share/apps/Amber/amber16//bin make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/nmr_aux' (cd nmode && make install) make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/nmode' cd ../lib && make rfree.o matinv.o nxtsec.o amopen.o rgroup.o cd ../lib && make sys.a cd ../blas && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lib' make[3]: 'rfree.o' is up to date. make[3]: 'matinv.o' is up to date. make[3]: 'nxtsec.o' is up to date. make[3]: 'amopen.o' is up to date. make[3]: 'rgroup.o' is up to date. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lib' gfortran -DBINTRAJ -DEMIL -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o /share/apps/Amber/amber16//bin/lmanal \ lmanal.o distr.o lmfil.o mexit.o count.o fluct.o lmdin.o dsort.o getref.o fileio.o corfl.o corfv.o rdparml.o ../lib/rfree.o ../lib/matinv.o ../lib/nxtsec.o ../lib/amopen.o ../lib/rgroup.o binpos.o \ -L/share/apps/Amber/amber16//lib -larpack -llapack -lblas -lxblas-amb make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lib' make[3]: 'sys.a' is up to date. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lib' make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/blas' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/blas' cd ../lapack && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/lapack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/lapack' cd ../arpack && make install make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/arpack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/arpack' gfortran -DBINTRAJ -DEMIL -fPIC -ffree-form -I/share/apps/Amber/amber16//include -I/share/apps/Amber/amber16//include -o /share/apps/Amber/amber16//bin/nmode \ nmode.o alloc.o angl.o assert.o bond.o bresna.o cdiv.o chck.o chdir.o chlamba.o debug.o decomp.o difang.o difbon.o dihdup.o dihed.o dirch.o dsort.o eigout.o ephi.o eprnt.o errstp.o findl.o forces.o getcor.o getf.o getm.o getref.o grdmax.o level.o lmdout.o lmode.o makel.o movecm.o mweight.o mweit.o new_stuff.o nmdfil.o nonbon.o nonbon1.o norm.o norml.o nrch.o oseen.o pairr.o pairw.o percon.o pload.o putvar.o rdinp.o rdparm.o remrot.o resdis.o savec.o savei.o savet.o setang.o setatm.o setbon.o setcor.o setdih.o setgam.o setgr.o setvar.o spsort.o thermo.o timit.o traco.o tsearch.o tstate.o xconst.o zerout.o zxcgr.o mexit.o ../lib/rfree.o ../lib/matinv.o ../lib/nxtsec.o ../lib/amopen.o ../lib/rgroup.o \ ../lib/sys.a -L/share/apps/Amber/amber16//lib -larpack -llapack -lblas -lxblas-amb make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/nmode' make build_cpptraj make[2]: Entering directory '/share/apps/Amber/amber16/AmberTools/src' (cd cpptraj && make install) make[3]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/cpptraj' cd src && make install make[4]: Entering directory '/share/apps/Amber/amber16/AmberTools/src/cpptraj/src' g++ -o cpptraj ActionFrameCounter.o ActionList.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_Hbond.o Action_Image.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_FFT.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o ComplexArray.o CoordinateInfo.o Corr.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataIO.o DataIO_CCP4.o DataIO_Cmatrix.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_double.o DataSet_float.o DataSet_integer.o DataSet_string.o Deprecated.o DihedralSearch.o DispatchObject.o DistRoutines.o Energy.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Exec_Analyze.o Exec_Calc.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_GenerateAmberRst.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrintData.o Exec_ReadData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_SequenceAlign.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_ViewRst.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_Std.o FileName.o FileTypes.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o InputTrajCommon.o KDE.o MapAtom.o MaskToken.o Matrix_3x3.o MetaData.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OutputTrajCommon.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o ProgressBar.o ProgressTimer.o PubFFT.o Random.o Range.o RPNcalc.o ReferenceAction.o Residue.o SDFfile.o SimplexMin.o Spline.o StringRoutines.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CIF.o Traj_Conflib.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o readline/libreadline.a -L/share/apps/Amber/amber16//lib -lfftw3 /share/apps/Amber/amber16//lib/libarpack.a /share/apps/Amber/amber16//lib/liblapack.a /share/apps/Amber/amber16//lib/libblas.a -lgfortran -w -L/share/apps/Amber/amber16//lib -lsander /share/apps/Amber/amber16//lib/libnetcdf.a -lbz2 -lz xdrfile/libxdrfile.a g++ -o ambpdb AmbPDB.o ActionFrameCounter.o ArgList.o Atom.o AtomMask.o BondSearch.o Box.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CIFfile.o CoordinateInfo.o CpptrajFile.o CpptrajStdio.o DistRoutines.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Std.o FileName.o FileTypes.o Frame.o InputTrajCommon.o MaskToken.o Matrix_3x3.o Mol2File.o NameType.o NC_Routines.o NetcdfFile.o OutputTrajCommon.o ParmFile.o Parm_Amber.o Parm_CIF.o Parm_CharmmPsf.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PDBfile.o ProgressBar.o Range.o SDFfile.o StringRoutines.o TextFormat.o TinkerFile.o Timer.o Topology.o TrajectoryFile.o TrajFrameCounter.o Trajin_Single.o Trajout_Single.o Residue.o Traj_AmberCoord.o Traj_AmberRestart.o Traj_CIF.o Traj_Mol2File.o Traj_SDF.o Traj_AmberNetcdf.o Traj_Binpos.o Traj_Conflib.o Traj_SQM.o Traj_AmberRestartNC.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_PDBfile.o Traj_Tinker.o Traj_NcEnsemble.o Vec3.o /share/apps/Amber/amber16//lib/libnetcdf.a -lbz2 -lz xdrfile/libxdrfile.a FileIO_Gzip.o: In function `FileIO_Gzip::Open(char const*, char const*)': FileIO_Gzip.cpp:(.text+0x13): undefined reference to `gzopen64' FileIO_Gzip.o: In function `FileIO_Gzip::Seek(long)': FileIO_Gzip.cpp:(.text+0x1fb): undefined reference to `gzseek64' FileIO_Gzip.o: In function `FileIO_Gzip::Tell()': FileIO_Gzip.cpp:(.text+0x235): undefined reference to `gztell64' collect2: error: ld returned 1 exit status Makefile:32: recipe for target 'ambpdb' failed make[4]: *** [ambpdb] Error 1 make[4]: *** Waiting for unfinished jobs.... FileIO_Gzip.o: In function `FileIO_Gzip::Open(char const*, char const*)': FileIO_Gzip.cpp:(.text+0x13): undefined reference to `gzopen64' FileIO_Gzip.o: In function `FileIO_Gzip::Seek(long)': FileIO_Gzip.cpp:(.text+0x1fb): undefined reference to `gzseek64' FileIO_Gzip.o: In function `FileIO_Gzip::Tell()': FileIO_Gzip.cpp:(.text+0x235): undefined reference to `gztell64' collect2: error: ld returned 1 exit status Makefile:25: recipe for target 'cpptraj' failed make[4]: *** [cpptraj] Error 1 make[4]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/cpptraj/src' Makefile:10: recipe for target 'install' failed make[3]: *** [install] Error 2 make[3]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src/cpptraj' Makefile:482: recipe for target 'build_cpptraj' failed make[2]: *** [build_cpptraj] Error 2 make[2]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src' Makefile:17: recipe for target 'serial' failed make[1]: *** [serial] Error 2 make[1]: Leaving directory '/share/apps/Amber/amber16/AmberTools/src' Makefile:7: recipe for target 'install' failed make: *** [install] Error 2