Problem: src/antechamber/bondtype.C fails to compile. The error message says that it can't find the vector header file "#include ", although the vector and vector.h are in /usr/include/g++-3/vector. The command from the makefile is: g++ -c -o bondtype.o bondtype.C When I add a "-I/usr/include/g++-3" to g++, I get the same error. Also, creating a symlink from /usr/include/c++/3.3.3 /usr/include/g++-3 doesn't help. The system is Redhat 7.3 w/ ifort, icc, and the Gnu c/c++ compilers installed. The ouput of the "make serial" command is as follows: -- Begin -- Starting installation of Amber8 (serial) at Fri Apr 22 13:01:47 EDT 2005. mkdir ../exe mkdir: cannot create directory `../exe': File exists make: [serial] Error 1 (ignored) cd lib; make install make[1]: Entering directory `/home/pmullins/amber8/src/lib' ifort -o new2oldparm new2oldparm.o nxtsec.o mv new2oldparm ../../exe /bin/rm _*.f /bin/rm: cannot remove `_*.f': No such file or directory make[1]: [install] Error 1 (ignored) make[1]: Leaving directory `/home/pmullins/amber8/src/lib' cd addles; make install make[1]: Entering directory `/home/pmullins/amber8/src/addles' cd ../lib; ./Makelist ../lib/random.o ../lib/mexit.o ../lib/nxtsec.o make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `random.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `mexit.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `nxtsec.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' ifort -o 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 les2prm.o checksz.o ../lib/random.o ../lib/mexit.o ../lib/nxtsec.o mv addles ../../exe make[1]: Leaving directory `/home/pmullins/amber8/src/addles' cd sander; make serial make[1]: Entering directory `/home/pmullins/amber8/src/sander' cd ../lib; make sys.a make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `sys.a' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' cd ../lib; make nxtsec.o make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `nxtsec.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' cd ../lapack; make make[2]: Entering directory `/home/pmullins/amber8/src/lapack' Makefile:7: warning: overriding commands for target `.f.o' ../config.h:79: warning: ignoring old commands for target `.f.o' ar rv lapack.a dsyev.o dlansy.o dsytrd.o dorgtr.o dsteqr.o dsterf.o dlascl.o dlamch.o xerbla.o ilaenv.o dlassq.o dsytd2.o dlatrd.o dorgql.o dorgqr.o dlasrt.o dlaset.o dlanst.o dlaev2.o dlasr.o dlapy2.o dlartg.o dlae2.o dorg2r.o dlarft.o dlarfb.o dorg2l.o dlarfg.o dlarf.o dspev.o dlansp.o dsptrd.o dopgtr.o dppsv.o dspsv.o dgeev.o dsptrs.o dsptrf.o dpptrs.o dpptrf.o dgebak.o dtrevc.o dlacpy.o dhseqr.o dorghr.o dgehrd.o dgebal.o dlange.o dlabad.o dlahqr.o dlarfx.o dlanhs.o dlaln2.o dgehd2.o dlahrd.o dlanv2.o dladiv.o dgerq2.o dorm2r.o dlarnv.o dgeqr2.o dlaruv.o dspevd.o dstedc.o dopmtr.o dlaed0.o dlaed1.o dlaed7.o dlaeda.o dlaed8.o dlaed9.o dlamrg.o dlaed2.o dlaed3.o dlaed4.o dlaed5.o dlaed6.o r - dsyev.o r - dlansy.o r - dsytrd.o r - dorgtr.o r - dsteqr.o r - dsterf.o r - dlascl.o r - dlamch.o r - xerbla.o r - ilaenv.o r - dlassq.o r - dsytd2.o r - dlatrd.o r - dorgql.o r - dorgqr.o r - dlasrt.o r - dlaset.o r - dlanst.o r - dlaev2.o r - dlasr.o r - dlapy2.o r - dlartg.o r - dlae2.o r - dorg2r.o r - dlarft.o r - dlarfb.o r - dorg2l.o r - dlarfg.o r - dlarf.o r - dspev.o r - dlansp.o r - dsptrd.o r - dopgtr.o r - dppsv.o r - dspsv.o r - dgeev.o r - dsptrs.o r - dsptrf.o r - dpptrs.o r - dpptrf.o r - dgebak.o r - dtrevc.o r - dlacpy.o r - dhseqr.o r - dorghr.o r - dgehrd.o r - dgebal.o r - dlange.o r - dlabad.o r - dlahqr.o r - dlarfx.o r - dlanhs.o r - dlaln2.o r - dgehd2.o r - dlahrd.o r - dlanv2.o r - dladiv.o r - dgerq2.o r - dorm2r.o r - dlarnv.o r - dgeqr2.o r - dlaruv.o r - dspevd.o r - dstedc.o r - dopmtr.o r - dlaed0.o r - dlaed1.o r - dlaed7.o r - dlaeda.o r - dlaed8.o r - dlaed9.o r - dlamrg.o r - dlaed2.o r - dlaed3.o r - dlaed4.o r - dlaed5.o r - dlaed6.o ranlib lapack.a make[2]: Leaving directory `/home/pmullins/amber8/src/lapack' cd ../blas; make make[2]: Entering directory `/home/pmullins/amber8/src/blas' Makefile:7: warning: overriding commands for target `.f.o' ../config.h:79: warning: ignoring old commands for target `.f.o' ar rv blas.a dasum.o daxpy.o dcabs1.o dcopy.o ddot.o dgbmv.o dgemm.o dgemv.o dger.o dnrm2.o drot.o drotg.o dsbmv.o dscal.o dspmv.o dspr.o dspr2.o dswap.o dsymm.o dsymv.o dsyr.o dsyr2.o dsyr2k.o dsyrk.o dtbmv.o dtbsv.o dtpmv.o dtpsv.o dtrmm.o dtrmv.o dtrsm.o dtrsv.o dummy.o dzasum.o dznrm2.o idamax.o isamax.o lsame.o r - dasum.o r - daxpy.o r - dcabs1.o r - dcopy.o r - ddot.o r - dgbmv.o r - dgemm.o r - dgemv.o r - dger.o r - dnrm2.o r - drot.o r - drotg.o r - dsbmv.o r - dscal.o r - dspmv.o r - dspr.o r - dspr2.o r - dswap.o r - dsymm.o r - dsymv.o r - dsyr.o r - dsyr2.o r - dsyr2k.o r - dsyrk.o r - dtbmv.o r - dtbsv.o r - dtpmv.o r - dtpsv.o r - dtrmm.o r - dtrmv.o r - dtrsm.o r - dtrsv.o r - dummy.o r - dzasum.o r - dznrm2.o r - idamax.o r - isamax.o r - lsame.o ranlib blas.a make[2]: Leaving directory `/home/pmullins/amber8/src/blas' cd ../lmod; make make[2]: Entering directory `/home/pmullins/amber8/src/lmod' cd xmin; make make[3]: Entering directory `/home/pmullins/amber8/src/lmod/xmin' Makefile:6: warning: overriding commands for target `.f.o' ../../config.h:79: warning: ignoring old commands for target `.f.o' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/home/pmullins/amber8/src/lmod/xmin' cd nvib; make make[3]: Entering directory `/home/pmullins/amber8/src/lmod/nvib' Makefile:6: warning: overriding commands for target `.f.o' ../../config.h:79: warning: ignoring old commands for target `.f.o' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/home/pmullins/amber8/src/lmod/nvib' cd lmod; make make[3]: Entering directory `/home/pmullins/amber8/src/lmod/lmod' Makefile:6: warning: overriding commands for target `.f.o' ../../config.h:79: warning: ignoring old commands for target `.f.o' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/home/pmullins/amber8/src/lmod/lmod' ar rv lmod.a xmin/*.o nvib/*.o lmod/*.o r - xmin/xmin.o r - nvib/nvib.o r - lmod/lmod.o ranlib lmod.a make[2]: Leaving directory `/home/pmullins/amber8/src/lmod' ifort -FR -o sander trace.o lmod.o decomp.o icosasurf.o egb.o findmask.o pb_force.o sander.o cshf.o noecalc.o noeread.o caldis.o calrate.o dinten.o drates.o indexn.o kmat.o pearsn.o plane.o remarc.o nmrcal.o nmrred.o restal.o getnat.o nmrnrg.o modwt.o disnrg.o angnrg.o tornrg.o nmrprt.o nmrgrp.o nmrcms.o nmrcmf.o impnum.o nmrsht.o at2res.o chklin.o opnmrg.o printe.o runmin.o ndvprt.o force.o rdparm.o mdread.o locmem.o runmd.o getcor.o r6ave.o r6drv.o aveint.o degcnt.o corf.o threeb.o tripl.o nmrrad.o decnvh.o fastwt.o echoin.o parallel.o jnrg.o shake.o ene.o mdwrit.o minrit.o set.o setmm.o dynlib.o mdfil.o nmlsrc.o ew_force.o ew_setup.o ew_box.o ew_bspline.o ew_fft.o ew_direct.o ew_recip.o pcshift.o align.o rstack.o istack.o rfree.o rgroup.o random.o lsqfit.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 mdm.o pb_init.o constantph.o prn_dipoles.o \ ../lmod/lmod.a \ ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o ../lib/sys.a ifort -FR -o sander.LES trace.o lmod.o decomp.o icosasurf.o egb.LES.o findmask.o pb_force.o sander.LES.o cshf.o noecalc.o noeread.o caldis.o calrate.o dinten.o drates.o indexn.o kmat.o pearsn.o plane.o remarc.o nmrcal.LES.o nmrred.LES.o restal.o getnat.o nmrnrg.o modwt.LES.o disnrg.o angnrg.o tornrg.o nmrprt.o nmrgrp.o nmrcms.o nmrcmf.o impnum.o nmrsht.o at2res.o chklin.o opnmrg.o printe.o runmin.o ndvprt.o force.LES.o rdparm.LES.o mdread.LES.o locmem.LES.o runmd.LES.o getcor.o r6ave.LES.o r6drv.o aveint.o degcnt.LES.o corf.o threeb.o tripl.o nmrrad.o decnvh.o fastwt.o echoin.o parallel.LES.o jnrg.LES.o shake.o ene.LES.o mdwrit.o minrit.o set.o setmm.o dynlib.LES.o mdfil.o nmlsrc.o ew_force.LES.o ew_setup.o ew_box.o ew_bspline.o ew_fft.o ew_direct.LES.o ew_recip.LES.o pcshift.o align.o rstack.o istack.o rfree.o rgroup.o random.o lsqfit.o amopen.o egb_les.LES.o debug.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o mexit.o new_time.o extra_pts.LES.o thermo_int.o matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o veclib.o mdm.o pb_init.o constantph.o prn_dipoles.o \ ../lmod/lmod.a \ ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o ../lib/sys.a cd ../divcon; make libdivcon.a make[2]: Entering directory `/home/pmullins/amber8/src/divcon' make[2]: `libdivcon.a' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/divcon' ifort -FR -o sander.QMMM trace.o debug.QMMM.o findmask.o pb_force.o sander.QMMM.o cshf.o noecalc.o noeread.o caldis.o calrate.o dinten.o drates.o indexn.o kmat.o pearsn.o plane.o remarc.o nmrcal.o nmrred.o restal.o getnat.o nmrnrg.o modwt.o disnrg.o angnrg.o tornrg.o nmrprt.o nmrgrp.o nmrcms.o nmrcmf.o impnum.o nmrsht.o at2res.o chklin.o opnmrg.o printe.QMMM.o runmin.QMMM.o ndvprt.o rdparm.QMMM.o mdread.QMMM.o locmem.QMMM.o runmd.QMMM.o getcor.QMMM.o r6ave.o r6drv.o aveint.o degcnt.o corf.o threeb.o tripl.o nmrrad.o decnvh.o fastwt.o echoin.o parallel.o jnrg.o shake.o ene.QMMM.o mdwrit.QMMM.o minrit.QMMM.o set.o setmm.o dynlib.o mdfil.o nmlsrc.o pcshift.o align.o rstack.o istack.o rfree.o rgroup.o random.o lsqfit.o amopen.o mexit.o new_time.o thermo_int.o matinv.o decomp.o assert.o erfcfun.o veclib.o mdm.o pb_init.o constantph.o prn_dipoles.o mmtsb.o mmtsb_client.o delbad.o link_atoms.o qmcompare.o qmsort.o forcecp.o ifshk.o resnba.o nonbon.o ../lib/nxtsec.o \ ../lapack/lapack.a ../blas/blas.a \ ../lib/sys.a ../divcon/libdivcon.a ../divcon/block.o cd ../lib; make mexit.o make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `mexit.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' ifort -FR -o ambmask ambmask.o findmask.o \ amopen.o ../lib/mexit.o ../lib/nxtsec.o /bin/mv sander sander.LES sander.QMMM ambmask ../../exe make[1]: Leaving directory `/home/pmullins/amber8/src/sander' cd ptraj; make install make[1]: Entering directory `/home/pmullins/amber8/src/ptraj' cd ../lapack; make make[2]: Entering directory `/home/pmullins/amber8/src/lapack' Makefile:7: warning: overriding commands for target `.f.o' ../config.h:79: warning: ignoring old commands for target `.f.o' ar rv lapack.a dsyev.o dlansy.o dsytrd.o dorgtr.o dsteqr.o dsterf.o dlascl.o dlamch.o xerbla.o ilaenv.o dlassq.o dsytd2.o dlatrd.o dorgql.o dorgqr.o dlasrt.o dlaset.o dlanst.o dlaev2.o dlasr.o dlapy2.o dlartg.o dlae2.o dorg2r.o dlarft.o dlarfb.o dorg2l.o dlarfg.o dlarf.o dspev.o dlansp.o dsptrd.o dopgtr.o dppsv.o dspsv.o dgeev.o dsptrs.o dsptrf.o dpptrs.o dpptrf.o dgebak.o dtrevc.o dlacpy.o dhseqr.o dorghr.o dgehrd.o dgebal.o dlange.o dlabad.o dlahqr.o dlarfx.o dlanhs.o dlaln2.o dgehd2.o dlahrd.o dlanv2.o dladiv.o dgerq2.o dorm2r.o dlarnv.o dgeqr2.o dlaruv.o dspevd.o dstedc.o dopmtr.o dlaed0.o dlaed1.o dlaed7.o dlaeda.o dlaed8.o dlaed9.o dlamrg.o dlaed2.o dlaed3.o dlaed4.o dlaed5.o dlaed6.o r - dsyev.o r - dlansy.o r - dsytrd.o r - dorgtr.o r - dsteqr.o r - dsterf.o r - dlascl.o r - dlamch.o r - xerbla.o r - ilaenv.o r - dlassq.o r - dsytd2.o r - dlatrd.o r - dorgql.o r - dorgqr.o r - dlasrt.o r - dlaset.o r - dlanst.o r - dlaev2.o r - dlasr.o r - dlapy2.o r - dlartg.o r - dlae2.o r - dorg2r.o r - dlarft.o r - dlarfb.o r - dorg2l.o r - dlarfg.o r - dlarf.o r - dspev.o r - dlansp.o r - dsptrd.o r - dopgtr.o r - dppsv.o r - dspsv.o r - dgeev.o r - dsptrs.o r - dsptrf.o r - dpptrs.o r - dpptrf.o r - dgebak.o r - dtrevc.o r - dlacpy.o r - dhseqr.o r - dorghr.o r - dgehrd.o r - dgebal.o r - dlange.o r - dlabad.o r - dlahqr.o r - dlarfx.o r - dlanhs.o r - dlaln2.o r - dgehd2.o r - dlahrd.o r - dlanv2.o r - dladiv.o r - dgerq2.o r - dorm2r.o r - dlarnv.o r - dgeqr2.o r - dlaruv.o r - dspevd.o r - dstedc.o r - dopmtr.o r - dlaed0.o r - dlaed1.o r - dlaed7.o r - dlaeda.o r - dlaed8.o r - dlaed9.o r - dlamrg.o r - dlaed2.o r - dlaed3.o r - dlaed4.o r - dlaed5.o r - dlaed6.o ranlib lapack.a make[2]: Leaving directory `/home/pmullins/amber8/src/lapack' cd ../arpack; make make[2]: Entering directory `/home/pmullins/amber8/src/arpack' Makefile:7: warning: overriding commands for target `.f.o' ../config.h:79: warning: ignoring old commands for target `.f.o' make[2]: Nothing to be done for `install'. make[2]: Leaving directory `/home/pmullins/amber8/src/arpack' cd ../blas; make make[2]: Entering directory `/home/pmullins/amber8/src/blas' Makefile:7: warning: overriding commands for target `.f.o' ../config.h:79: warning: ignoring old commands for target `.f.o' ar rv blas.a dasum.o daxpy.o dcabs1.o dcopy.o ddot.o dgbmv.o dgemm.o dgemv.o dger.o dnrm2.o drot.o drotg.o dsbmv.o dscal.o dspmv.o dspr.o dspr2.o dswap.o dsymm.o dsymv.o dsyr.o dsyr2.o dsyr2k.o dsyrk.o dtbmv.o dtbsv.o dtpmv.o dtpsv.o dtrmm.o dtrmv.o dtrsm.o dtrsv.o dummy.o dzasum.o dznrm2.o idamax.o isamax.o lsame.o r - dasum.o r - daxpy.o r - dcabs1.o r - dcopy.o r - ddot.o r - dgbmv.o r - dgemm.o r - dgemv.o r - dger.o r - dnrm2.o r - drot.o r - drotg.o r - dsbmv.o r - dscal.o r - dspmv.o r - dspr.o r - dspr2.o r - dswap.o r - dsymm.o r - dsymv.o r - dsyr.o r - dsyr2.o r - dsyr2k.o r - dsyrk.o r - dtbmv.o r - dtbsv.o r - dtpmv.o r - dtpsv.o r - dtrmm.o r - dtrmv.o r - dtrsm.o r - dtrsv.o r - dummy.o r - dzasum.o r - dznrm2.o r - idamax.o r - isamax.o r - lsame.o ranlib blas.a make[2]: Leaving directory `/home/pmullins/amber8/src/blas' cd ../lib ; make sys.a make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `sys.a' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' cd pdb; make make[2]: Entering directory `/home/pmullins/amber8/src/ptraj/pdb' make[2]: Nothing to be done for `install'. make[2]: Leaving directory `/home/pmullins/amber8/src/ptraj/pdb' ifort -nofor_main -FR -o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o io.o trajectory.o evec.o torsion.o rms.o display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o pdb/libpdb.a ../arpack/arpack.a ../lapack/lapack.a ../blas/blas.a ifort -nofor_main -FR -o ptraj main.o rdparm.o dispatch.o help.o utility.o second.o io.o trajectory.o evec.o torsion.o rms.o display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o pdb/libpdb.a ../arpack/arpack.a ../lapack/lapack.a ../blas/blas.a /bin/mv rdparm ptraj ../../exe make[1]: Leaving directory `/home/pmullins/amber8/src/ptraj' cd nmr_aux; make install make[1]: Entering directory `/home/pmullins/amber8/src/nmr_aux' cd prepare_input; make clean ; make install make[2]: Entering directory `/home/pmullins/amber8/src/nmr_aux/prepare_input' /bin/rm *.o _*.f makeDIST_RST makeANG_RST makeSHF.cp makeCHIR_RST.cp \ makeDIP_RST.protein.cp makeDIP_RST.dna.cp /bin/rm: cannot remove `_*.f': No such file or directory /bin/rm: cannot remove `makeDIST_RST': No such file or directory /bin/rm: cannot remove `makeANG_RST': No such file or directory /bin/rm: cannot remove `makeSHF.cp': No such file or directory /bin/rm: cannot remove `makeCHIR_RST.cp': No such file or directory /bin/rm: cannot remove `makeDIP_RST.protein.cp': No such file or directory /bin/rm: cannot remove `makeDIP_RST.dna.cp': No such file or directory make[2]: [clean] Error 1 (ignored) make[2]: Leaving directory `/home/pmullins/amber8/src/nmr_aux/prepare_input' make[2]: Entering directory `/home/pmullins/amber8/src/nmr_aux/prepare_input' gcc -c -O2 -o makeDIST_RST.o makeDIST_RST.c gcc -o makeDIST_RST makeDIST_RST.o -lm gcc -c -O2 -o makeANG_RST.o makeANG_RST.c gcc -o makeANG_RST makeANG_RST.o -lm /bin/rm -f makeSHF_RST.cp makeCHIR_RST.cp makeDIP_RST.protein.cp \ makeDIP_RST.dna.cp cp makeSHF_RST makeSHF_RST.cp cp makeCHIR_RST makeCHIR_RST.cp cp makeDIP_RST.protein makeDIP_RST.protein.cp cp makeDIP_RST.dna makeDIP_RST.dna.cp chmod 755 makeDIST_RST makeANG_RST makeSHF_RST.cp makeCHIR_RST.cp \ makeDIP_RST.protein.cp makeDIP_RST.dna.cp mv makeDIST_RST makeANG_RST ../../../exe mv makeCHIR_RST.cp ../../../exe/makeCHIR_RST mv makeSHF_RST.cp ../../../exe/makeSHF_RST mv makeDIP_RST.protein.cp ../../../exe/makeDIP_RST.protein mv makeDIP_RST.dna.cp ../../../exe/makeDIP_RST.dna cp map.DG-AMBER ../../../dat cp map.Brook-AMBER ../../../dat make[2]: Leaving directory `/home/pmullins/amber8/src/nmr_aux/prepare_input' cd fantasian; make clean ; make install make[2]: Entering directory `/home/pmullins/amber8/src/nmr_aux/fantasian' /bin/rm *.o _*.f fantasian /bin/rm: cannot remove `fantasian': No such file or directory make[2]: [clean] Error 1 (ignored) make[2]: Leaving directory `/home/pmullins/amber8/src/nmr_aux/fantasian' make[2]: Entering directory `/home/pmullins/amber8/src/nmr_aux/fantasian' cpp -traditional -P -I/home/pmullins/amber8/src/include fantasian.f > _fantasian.f ifort -c -w95 -mp1 -O0 -o fantasian.o _fantasian.f ifort -o fantasian fantasian.o ../../lib/random.o ../../lib/mexit.o mv fantasian ../../../exe/ make[2]: Leaving directory `/home/pmullins/amber8/src/nmr_aux/fantasian' cp senergy sviol sviol2 ../../exe make[1]: Leaving directory `/home/pmullins/amber8/src/nmr_aux' cd nmode; make install make[1]: Entering directory `/home/pmullins/amber8/src/nmode' cd ../lib ; ./Makelist ../lib/rfree.o ../lib/matinv.o ../lib/nxtsec.o ../lib/amopen.o make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `rfree.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `matinv.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `nxtsec.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `amopen.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' cd ../lib; make sys.a make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `sys.a' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' cd ../lapack; make make[2]: Entering directory `/home/pmullins/amber8/src/lapack' Makefile:7: warning: overriding commands for target `.f.o' ../config.h:79: warning: ignoring old commands for target `.f.o' ar rv lapack.a dsyev.o dlansy.o dsytrd.o dorgtr.o dsteqr.o dsterf.o dlascl.o dlamch.o xerbla.o ilaenv.o dlassq.o dsytd2.o dlatrd.o dorgql.o dorgqr.o dlasrt.o dlaset.o dlanst.o dlaev2.o dlasr.o dlapy2.o dlartg.o dlae2.o dorg2r.o dlarft.o dlarfb.o dorg2l.o dlarfg.o dlarf.o dspev.o dlansp.o dsptrd.o dopgtr.o dppsv.o dspsv.o dgeev.o dsptrs.o dsptrf.o dpptrs.o dpptrf.o dgebak.o dtrevc.o dlacpy.o dhseqr.o dorghr.o dgehrd.o dgebal.o dlange.o dlabad.o dlahqr.o dlarfx.o dlanhs.o dlaln2.o dgehd2.o dlahrd.o dlanv2.o dladiv.o dgerq2.o dorm2r.o dlarnv.o dgeqr2.o dlaruv.o dspevd.o dstedc.o dopmtr.o dlaed0.o dlaed1.o dlaed7.o dlaeda.o dlaed8.o dlaed9.o dlamrg.o dlaed2.o dlaed3.o dlaed4.o dlaed5.o dlaed6.o r - dsyev.o r - dlansy.o r - dsytrd.o r - dorgtr.o r - dsteqr.o r - dsterf.o r - dlascl.o r - dlamch.o r - xerbla.o r - ilaenv.o r - dlassq.o r - dsytd2.o r - dlatrd.o r - dorgql.o r - dorgqr.o r - dlasrt.o r - dlaset.o r - dlanst.o r - dlaev2.o r - dlasr.o r - dlapy2.o r - dlartg.o r - dlae2.o r - dorg2r.o r - dlarft.o r - dlarfb.o r - dorg2l.o r - dlarfg.o r - dlarf.o r - dspev.o r - dlansp.o r - dsptrd.o r - dopgtr.o r - dppsv.o r - dspsv.o r - dgeev.o r - dsptrs.o r - dsptrf.o r - dpptrs.o r - dpptrf.o r - dgebak.o r - dtrevc.o r - dlacpy.o r - dhseqr.o r - dorghr.o r - dgehrd.o r - dgebal.o r - dlange.o r - dlabad.o r - dlahqr.o r - dlarfx.o r - dlanhs.o r - dlaln2.o r - dgehd2.o r - dlahrd.o r - dlanv2.o r - dladiv.o r - dgerq2.o r - dorm2r.o r - dlarnv.o r - dgeqr2.o r - dlaruv.o r - dspevd.o r - dstedc.o r - dopmtr.o r - dlaed0.o r - dlaed1.o r - dlaed7.o r - dlaeda.o r - dlaed8.o r - dlaed9.o r - dlamrg.o r - dlaed2.o r - dlaed3.o r - dlaed4.o r - dlaed5.o r - dlaed6.o ranlib lapack.a make[2]: Leaving directory `/home/pmullins/amber8/src/lapack' cd ../blas; make make[2]: Entering directory `/home/pmullins/amber8/src/blas' Makefile:7: warning: overriding commands for target `.f.o' ../config.h:79: warning: ignoring old commands for target `.f.o' ar rv blas.a dasum.o daxpy.o dcabs1.o dcopy.o ddot.o dgbmv.o dgemm.o dgemv.o dger.o dnrm2.o drot.o drotg.o dsbmv.o dscal.o dspmv.o dspr.o dspr2.o dswap.o dsymm.o dsymv.o dsyr.o dsyr2.o dsyr2k.o dsyrk.o dtbmv.o dtbsv.o dtpmv.o dtpsv.o dtrmm.o dtrmv.o dtrsm.o dtrsv.o dummy.o dzasum.o dznrm2.o idamax.o isamax.o lsame.o r - dasum.o r - daxpy.o r - dcabs1.o r - dcopy.o r - ddot.o r - dgbmv.o r - dgemm.o r - dgemv.o r - dger.o r - dnrm2.o r - drot.o r - drotg.o r - dsbmv.o r - dscal.o r - dspmv.o r - dspr.o r - dspr2.o r - dswap.o r - dsymm.o r - dsymv.o r - dsyr.o r - dsyr2.o r - dsyr2k.o r - dsyrk.o r - dtbmv.o r - dtbsv.o r - dtpmv.o r - dtpsv.o r - dtrmm.o r - dtrmv.o r - dtrsm.o r - dtrsv.o r - dummy.o r - dzasum.o r - dznrm2.o r - idamax.o r - isamax.o r - lsame.o ranlib blas.a make[2]: Leaving directory `/home/pmullins/amber8/src/blas' ifort -FR -o nmode nmode.o alloc.o angl.o assert.o bond.o bresna.o cdiv.o chck.o chdir.o chlamba.o debug.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 rgroup.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/sys.a ../lapack/lapack.a ../blas/blas.a /bin/mv nmode ../../exe make[1]: Leaving directory `/home/pmullins/amber8/src/nmode' cd resp; make install make[1]: Entering directory `/home/pmullins/amber8/src/resp' cd ../lib ; ./Makelist ../lib/mexit.o ../lib/amopen.o ../lib/lapack.o make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `mexit.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `amopen.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `lapack.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' cd ../lib ; make sys.a make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `sys.a' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' ifort -o resp resp.o ../lib/mexit.o ../lib/amopen.o ../lib/lapack.o ../lib/sys.a /bin/mv resp ../../exe/ make[1]: Leaving directory `/home/pmullins/amber8/src/resp' cd protonate; make install make[1]: Entering directory `/home/pmullins/amber8/src/protonate' cd ../lib ; ./Makelist ../lib/mexit.o ../lib/amopen.o make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `mexit.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `amopen.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' cd ../lib; make sys.a make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `sys.a' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' ifort -o pol_h pol_h.o stm_sel.o sortf_as.o ../lib/mexit.o ../lib/amopen.o ../lib/sys.a ifort -o protonate protonate.o ../lib/mexit.o ../lib/amopen.o ../lib/sys.a ifort -o gwh gwh.o pdbatm.o pdbhet2.o top_3.o stm_sel.o sortf_as.o ../lib/mexit.o ../lib/amopen.o ../lib/sys.a mv pol_h protonate gwh ../../exe/ make[1]: Leaving directory `/home/pmullins/amber8/src/protonate' cd anal; make install make[1]: Entering directory `/home/pmullins/amber8/src/anal' cd ../lib ; ./Makelist ../lib/rfree.o ../lib/rgroup.o ../lib/nxtsec.o ../lib/util.o ../lib/amopen.o ../lib/mexit.o ../lib/ligenb.o make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `rfree.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `rgroup.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `nxtsec.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `util.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `amopen.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `mexit.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `ligenb.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' cd ../lib; make sys.a make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `sys.a' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' ifort -o anal anafil.o analgr.o analys.o angl.o anglp.o atmget.o bangle.o bond.o bpgen.o calhb.o calhx.o calpuc.o chain.o clear.o compact.o dihtel.o dist.o egout.o egrout.o ephi.o gaus80.o gauss.o getall.o getcmn.o hangl.o haxis.o hbond.o hbout.o helix.o locmem.o lsqstr.o matind.o mdbox.o mdread.o minv.o movecm.o nhbpar.o pdbout.o pdbrit.o percon.o prtri.o prtrin.o puck.o pucker.o radgy.o rdparm.o rdrest.o resdis.o resnbn.o resnbp.o rms.o rmsfit.o rmsmov.o stell.o stogrd.o sumgrp.o teldih.o telint.o tell.o tilang.o tilt.o tors.o traco.o vect.o volume.o xconst.o ../lib/rfree.o ../lib/rgroup.o ../lib/nxtsec.o ../lib/util.o ../lib/amopen.o ../lib/mexit.o ../lib/ligenb.o ../lib/sys.a /bin/mv anal ../../exe/ make[1]: Leaving directory `/home/pmullins/amber8/src/anal' cd mm_pbsa; make install make[1]: Entering directory `/home/pmullins/amber8/src/mm_pbsa' ifort -o make_crd_hg make_crd_hg.o ../lib/amopen.o ../lib/mexit.o gcc -O2 -o molsurf molsurf.o -lm mv make_crd_hg molsurf ../../exe cp mm_pbsa.pl mm_pbsa_statistics.pl ../../exe make[1]: Leaving directory `/home/pmullins/amber8/src/mm_pbsa' cd pbsa; make install make[1]: Entering directory `/home/pmullins/amber8/src/pbsa' cd ../lmod; make make[2]: Entering directory `/home/pmullins/amber8/src/lmod' cd xmin; make make[3]: Entering directory `/home/pmullins/amber8/src/lmod/xmin' Makefile:6: warning: overriding commands for target `.f.o' ../../config.h:79: warning: ignoring old commands for target `.f.o' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/home/pmullins/amber8/src/lmod/xmin' cd nvib; make make[3]: Entering directory `/home/pmullins/amber8/src/lmod/nvib' Makefile:6: warning: overriding commands for target `.f.o' ../../config.h:79: warning: ignoring old commands for target `.f.o' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/home/pmullins/amber8/src/lmod/nvib' cd lmod; make make[3]: Entering directory `/home/pmullins/amber8/src/lmod/lmod' Makefile:6: warning: overriding commands for target `.f.o' ../../config.h:79: warning: ignoring old commands for target `.f.o' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/home/pmullins/amber8/src/lmod/lmod' ar rv lmod.a xmin/*.o nvib/*.o lmod/*.o r - xmin/xmin.o r - nvib/nvib.o r - lmod/lmod.o ranlib lmod.a make[2]: Leaving directory `/home/pmullins/amber8/src/lmod' cd ../lib; make sys.a make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `sys.a' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' cd ../lib; make nxtsec.o make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `nxtsec.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' cd ../lapack; make make[2]: Entering directory `/home/pmullins/amber8/src/lapack' Makefile:7: warning: overriding commands for target `.f.o' ../config.h:79: warning: ignoring old commands for target `.f.o' ar rv lapack.a dsyev.o dlansy.o dsytrd.o dorgtr.o dsteqr.o dsterf.o dlascl.o dlamch.o xerbla.o ilaenv.o dlassq.o dsytd2.o dlatrd.o dorgql.o dorgqr.o dlasrt.o dlaset.o dlanst.o dlaev2.o dlasr.o dlapy2.o dlartg.o dlae2.o dorg2r.o dlarft.o dlarfb.o dorg2l.o dlarfg.o dlarf.o dspev.o dlansp.o dsptrd.o dopgtr.o dppsv.o dspsv.o dgeev.o dsptrs.o dsptrf.o dpptrs.o dpptrf.o dgebak.o dtrevc.o dlacpy.o dhseqr.o dorghr.o dgehrd.o dgebal.o dlange.o dlabad.o dlahqr.o dlarfx.o dlanhs.o dlaln2.o dgehd2.o dlahrd.o dlanv2.o dladiv.o dgerq2.o dorm2r.o dlarnv.o dgeqr2.o dlaruv.o dspevd.o dstedc.o dopmtr.o dlaed0.o dlaed1.o dlaed7.o dlaeda.o dlaed8.o dlaed9.o dlamrg.o dlaed2.o dlaed3.o dlaed4.o dlaed5.o dlaed6.o r - dsyev.o r - dlansy.o r - dsytrd.o r - dorgtr.o r - dsteqr.o r - dsterf.o r - dlascl.o r - dlamch.o r - xerbla.o r - ilaenv.o r - dlassq.o r - dsytd2.o r - dlatrd.o r - dorgql.o r - dorgqr.o r - dlasrt.o r - dlaset.o r - dlanst.o r - dlaev2.o r - dlasr.o r - dlapy2.o r - dlartg.o r - dlae2.o r - dorg2r.o r - dlarft.o r - dlarfb.o r - dorg2l.o r - dlarfg.o r - dlarf.o r - dspev.o r - dlansp.o r - dsptrd.o r - dopgtr.o r - dppsv.o r - dspsv.o r - dgeev.o r - dsptrs.o r - dsptrf.o r - dpptrs.o r - dpptrf.o r - dgebak.o r - dtrevc.o r - dlacpy.o r - dhseqr.o r - dorghr.o r - dgehrd.o r - dgebal.o r - dlange.o r - dlabad.o r - dlahqr.o r - dlarfx.o r - dlanhs.o r - dlaln2.o r - dgehd2.o r - dlahrd.o r - dlanv2.o r - dladiv.o r - dgerq2.o r - dorm2r.o r - dlarnv.o r - dgeqr2.o r - dlaruv.o r - dspevd.o r - dstedc.o r - dopmtr.o r - dlaed0.o r - dlaed1.o r - dlaed7.o r - dlaeda.o r - dlaed8.o r - dlaed9.o r - dlamrg.o r - dlaed2.o r - dlaed3.o r - dlaed4.o r - dlaed5.o r - dlaed6.o ranlib lapack.a make[2]: Leaving directory `/home/pmullins/amber8/src/lapack' cd ../blas; make make[2]: Entering directory `/home/pmullins/amber8/src/blas' Makefile:7: warning: overriding commands for target `.f.o' ../config.h:79: warning: ignoring old commands for target `.f.o' ar rv blas.a dasum.o daxpy.o dcabs1.o dcopy.o ddot.o dgbmv.o dgemm.o dgemv.o dger.o dnrm2.o drot.o drotg.o dsbmv.o dscal.o dspmv.o dspr.o dspr2.o dswap.o dsymm.o dsymv.o dsyr.o dsyr2.o dsyr2k.o dsyrk.o dtbmv.o dtbsv.o dtpmv.o dtpsv.o dtrmm.o dtrmv.o dtrsm.o dtrsv.o dummy.o dzasum.o dznrm2.o idamax.o isamax.o lsame.o r - dasum.o r - daxpy.o r - dcabs1.o r - dcopy.o r - ddot.o r - dgbmv.o r - dgemm.o r - dgemv.o r - dger.o r - dnrm2.o r - drot.o r - drotg.o r - dsbmv.o r - dscal.o r - dspmv.o r - dspr.o r - dspr2.o r - dswap.o r - dsymm.o r - dsymv.o r - dsyr.o r - dsyr2.o r - dsyr2k.o r - dsyrk.o r - dtbmv.o r - dtbsv.o r - dtpmv.o r - dtpsv.o r - dtrmm.o r - dtrmv.o r - dtrsm.o r - dtrsv.o r - dummy.o r - dzasum.o r - dznrm2.o r - idamax.o r - isamax.o r - lsame.o ranlib blas.a make[2]: Leaving directory `/home/pmullins/amber8/src/blas' ifort -FR -o pbsa pbsa.o runmd.o runmin.o lmod.o mdread.o rdparm.o getcor.o force.o pb_force.o pb_init.o egb.o ene.o decomp.o icosasurf.o findmask.o printe.o locmem.o fastwt.o echoin.o parallel.o shake.o mdwrit.o minrit.o set.o setmm.o dynlib.o mdfil.o nmlsrc.o rstack.o istack.o rfree.o rgroup.o random.o amopen.o debug.o degcnt.o mexit.o new_time.o matinv.o assert.o veclib.o constantph.o ../lmod/lmod.a ../lib/sys.a ../lib/nxtsec.o \ ../lapack/lapack.a ../blas/blas.a /bin/mv pbsa ../../exe make[1]: Leaving directory `/home/pmullins/amber8/src/pbsa' cd etc; make install make[1]: Entering directory `/home/pmullins/amber8/src/etc' cd ../lib ; ./Makelist ../lib/amopen.o ../lib/mexit.o ../lib/nxtsec.o make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `amopen.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `mexit.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `nxtsec.o' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' ifort -o ambpdb ambpdb.o forFIRSTtype.o forFIRSTbond.o forFIRSThbond.o forFIRSTteth.o forFIRSToutp.o ../lib/amopen.o ../lib/mexit.o ../lib/nxtsec.o ifort -o nucgen nucgen.o ngfil.o ../lib/amopen.o ../lib/mexit.o ../lib/nxtsec.o \ ../lib/sys.a /bin/mv ambpdb nucgen ../../exe/ /bin/cp calcpka.pl cpinutil.pl CPin.pm ../../exe make[1]: Leaving directory `/home/pmullins/amber8/src/etc' cd divcon; make install make[1]: Entering directory `/home/pmullins/amber8/src/divcon' cd ../lib; make sys.a make[2]: Entering directory `/home/pmullins/amber8/src/lib' make[2]: `sys.a' is up to date. make[2]: Leaving directory `/home/pmullins/amber8/src/lib' ifort -o divcon assign.o atgrid.o atmchg.o atmlist.o av.o bcheck.o bleng.o block.o bndang.o boxmove.o boxstep.o bpair.o bsort.o bsrch.o balance.o bspline.o calcgeo.o chkovlp.o chkres.o clustsub.o cmbcore.o cmbsub.o denful.o densub.o diag.o diagp.o diat.o dihedr.o diisub.o diislb.o dipole.o doferm.o dograd.o doscfdc.o densubfdm.o edriver.o energydc.o error.o escf.o esqr.o esqrfdm.o etimer.o fmix.o fockdc.o freq.o frmchk.o fshift.o g2int.o gcart.o gensub.o geoopt.o getcrd.o getdir.o getpar.o getpep.o getrforc.o getxyz.o glbpnt.o gridafnc.o gridrfnc.o header.o homolumo.o hsep.o icoord.o ijpair.o initp.o intpr.o lbfgs.o linmin.o lsolve.o math.o mixgrid.o mkgrid.o mosub.o mosubfdm.o mosubfdmx.o mvcrd.o namemcf.o opnfil.o overlp.o pbcxyz.o pgridrfnc.o pgridafnc.o printsub.o pmix.o prjfc.o printpar.o push.o rdalldc.o rdbelly.o rdbox.o rdcluster.o rdcomb.o rdgrid.o rdgroup.o rdint.o rdkeys.o rdnext.o rdnum.o rdrst.o rdsub.o rdword.o rdxyz.o resgrid.o rcalc.o rdtail.o rdlist.o repul.o random.o rotate.o rdguess.o rddmx.o rdneighb.o rdpdb.o rddos.o rdprtvec.o rdhess.o septs.o setbox.o setncell.o setup.o setunit.o sproc.o stripkeywd.o setdef.o setopt.o setprtvec.o sabt.o tsqna.o tsrfo.o upcase.o wdjoin.o whatis.o wrtchg.o wrtgrd.o wrthss.o wrtint.o wrtpdb.o wrtrst.o wrtvec.o wrtcoor.o wrtxyz.o wrttim.o wrtdiv.o wrtdmx.o wrtvecsub.o zmake.o divcon.o ../lib/sys.a mv divcon ../../exe make[1]: Leaving directory `/home/pmullins/amber8/src/divcon' cd antechamber; make install make[1]: Entering directory `/home/pmullins/amber8/src/antechamber' g++ -c -o bondtype.o bondtype.C bondtype.C:23:19: vector: No such file or directory bondtype.C:79: error: `vector' not declared bondtype.C:242: error: `vector' was not declared in this scope bondtype.C:242: error: parse error before `>' token bondtype.C: In function `void get_penalties(...)': bondtype.C:250: error: `penalties' undeclared (first use this function) bondtype.C:250: error: (Each undeclared identifier is reported only once for each function it appears in.) bondtype.C: At global scope: bondtype.C:254: error: `vector' was not declared in this scope bondtype.C:254: error: parse error before `>' token bondtype.C:257: error: 'vector' is used as a type, but is not defined as a type. bondtype.C:258: error: parse error before `for' bondtype.C:258: error: `points' was not declared in this scope bondtype.C:258: error: parse error before `;' token bondtype.C:258: error: syntax error before `++' token bondtype.C:264: error: `vector' was not declared in this scope bondtype.C:264: error: parse error before `>' token bondtype.C: In function `bool check_exist(...)': bondtype.C:267: error: `addrs1' undeclared (first use this function) bondtype.C:268: error: `addrs2' undeclared (first use this function) bondtype.C: At global scope: bondtype.C:278: error: `vector' was not declared in this scope bondtype.C:278: error: parse error before `>' token bondtype.C:284: error: parse error before `;' token bondtype.C:284: error: syntax error before `++' token bondtype.C:286: error: syntax error before `.' token bondtype.C:287: error: syntax error before `.' token bondtype.C:290: error: `n' was not declared in this scope bondtype.C:290: error: parse error before `;' token bondtype.C:290: error: syntax error before `++' token bondtype.C:292: error: syntax error before `.' token bondtype.C:293: error: syntax error before `.' token bondtype.C:296: error: syntax error before `<=' token bondtype.C:296: error: syntax error before `++' token bondtype.C:299: error: `vector' was not declared in this scope bondtype.C:299: error: parse error before `>' token bondtype.C:302: error: `r1' was not declared in this scope bondtype.C:302: error: parse error before `;' token bondtype.C:302: error: syntax error before `++' token bondtype.C:303: error: `r2' was not declared in this scope bondtype.C:303: error: parse error before `;' token bondtype.C:303: error: syntax error before `++' token bondtype.C:305: error: parse error before `=' token bondtype.C:308: error: parse error before `if' bondtype.C:310: error: `r2' was not declared in this scope bondtype.C:310: error: `y' was not declared in this scope bondtype.C:310: error: parse error before `;' token bondtype.C:310: error: syntax error before `++' token bondtype.C:313: error: syntax error before `.' token bondtype.C:322: error: `vector' was not declared in this scope bondtype.C:322: error: `vector' was not declared in this scope bondtype.C:322: error: parse error before `>' token bondtype.C: In function `void dump(...)': bondtype.C:325: error: `array' undeclared (first use this function) bondtype.C: At global scope: bondtype.C:348: error: `vector' was not declared in this scope bondtype.C:348: error: `vector' was not declared in this scope bondtype.C:348: error: parse error before `>' token bondtype.C:372: error: `vector' was not declared in this scope bondtype.C:372: error: `vector' was not declared in this scope bondtype.C:372: error: parse error before `>' token bondtype.C: In function `void dumplication(...)': bondtype.C:376: error: `vector' undeclared (first use this function) bondtype.C:376: error: parse error before `>' token bondtype.C:379: error: request for member `push_back' in `index', which is of non-aggregate type `char*()(const char*, int) throw ()' bondtype.C:381: error: pointer to a function used in arithmetic bondtype.C:385: error: pointer to a function used in arithmetic bondtype.C:399: error: pointer to a function used in arithmetic bondtype.C:399: error: assignment of read-only location bondtype.C:399: error: cannot convert `int' to `char*()(const char*, int)' in assignment bondtype.C:403: error: pointer to a function used in arithmetic bondtype.C: In function `int main(int, char**)': bondtype.C:1097: error: parse error before `>' token bondtype.C:1098: error: parse error before `>' token bondtype.C:1106: error: `tmparray' undeclared (first use this function) bondtype.C:1106: error: `process_penalties' undeclared (first use this function) make[1]: *** [bondtype.o] Error 1 make[1]: Leaving directory `/home/pmullins/amber8/src/antechamber' make: *** [serial] Error 2 -- End --