AMBER Archive (2009)

Subject: [AMBER] AmberTools compiling error

From: Farly Walsh (farlyw_at_gmail.com)
Date: Sun Apr 26 2009 - 19:40:38 CDT

HI all!

May be somebody got the same error after running "make -f Makefile_at":

sed -e "s?BINDIR?/home/lparsons/build_amber/bin?" mopac.sh >
/home/lparsons/build_amber/bin/mopac.sh
chmod +x /home/lparsons/build_amber/bin/mopac.sh
mv -f am1bcc acdoctor antechamber atomtype bondtype charmmgen database
espgen parmcal parmchk prepgen residuegen respgen translate top2mol2
/home/lparsons/build_amber/bin
make[1]: Leaving directory `/home/lparsons/build_amber/src/antechamber'
(cd mopac6/src && make hasG77 )
make[1]: Entering directory `/home/lparsons/build_amber/src/mopac6/src'
g77 aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o
block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o
compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o
depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o
deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o
diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o
drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o
fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o
geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o
grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o
iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o
matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o
mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o
polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o
repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o
swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o
wrttxt.o xyzint.o -o mopac
mv mopac /home/lparsons/build_amber/bin
make[1]: Leaving directory `/home/lparsons/build_amber/src/mopac6/src'
(cd resp && make hasG77 )
make[1]: Entering directory `/home/lparsons/build_amber/src/resp'
g77 lapack.o resp.o -o resp
mv resp /home/lparsons/build_amber/bin
make[1]: Leaving directory `/home/lparsons/build_amber/src/resp'
(cd ptraj && make install )
make[1]: Entering directory `/home/lparsons/build_amber/src/ptraj'
Makefile:24: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
gcc -o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o io.o
trajectory.o evec.o torsion.o mask.o rms.o display.o interface.o
energy.o experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o
cluster.o clusterLib.o /home/lparsons/build_amber/lib/libpdb.a
/home/lparsons/build_amber/lib/libsym.a
/home/lparsons/build_amber/lib/arpack.a
/home/lparsons/build_amber/lib/lapack.a
/home/lparsons/build_amber/lib/blas.a
/home/lparsons/build_amber/lib/f2c.a ../netcdf/lib/libnetcdf.a -lm
ptraj.o: In function `checkCoordinates':
ptraj.c:(.text+0x7115): undefined reference to `netcdfGetAttributeText'
ptraj.c:(.text+0x713b): undefined reference to `netcdfGetAttributeText'
ptraj.c:(.text+0x7161): undefined reference to `netcdfGetAttributeText'
ptraj.c:(.text+0x718a): undefined reference to `netcdfGetAttributeText'
ptraj.c:(.text+0x71b3): undefined reference to `netcdfGetAttributeText'
ptraj.o:ptraj.c:(.text+0x71d9): more undefined references to
`netcdfGetAttributeText' follow
ptraj.o: In function `checkCoordinates':
ptraj.c:(.text+0x7270): undefined reference to `netcdfGetDimensionInfo'
ptraj.c:(.text+0x7296): undefined reference to `netcdfGetDimensionInfo'
ptraj.c:(.text+0x72bc): undefined reference to `netcdfGetDimensionInfo'
ptraj.o: In function `ptrajOutputCoordinates':
ptraj.c:(.text+0xf2d0): undefined reference to `netcdfPutAttributeText'
ptraj.c:(.text+0xf2f3): undefined reference to `netcdfPutAttributeText'
ptraj.c:(.text+0xf319): undefined reference to `netcdfPutAttributeText'
ptraj.c:(.text+0xf33f): undefined reference to `netcdfPutAttributeText'
ptraj.c:(.text+0xf35c): undefined reference to `netcdfPutAttributeText'
ptraj.o:ptraj.c:(.text+0xf379): more undefined references to
`netcdfPutAttributeText' follow
collect2: ld returned 1 exit status
make[1]: *** [rdparm] Error 1
make[1]: Leaving directory `/home/lparsons/build_amber/src/ptraj'
make: *** [install] Error 2

I hope that you can help me guys. I am really stuck with this problem.

Thank you,

Farly
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