AMBER Archive (2009)

Subject: [AMBER] question

From: Tatyana Fedotova (FedotovT_at_upstate.edu)
Date: Fri Apr 24 2009 - 14:55:40 CDT

Dear Mrs/Sir,

My name is Tatyana.
I am compiling AMBERTools now and I ran into the problem with that.

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

Could you help me with that if you've seen the same message error.

Thank you,

Sincerely,

Tanya

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber