AMBER: PMEMD compilation error

From: Joseph Fernandez <>
Date: Mon, 8 May 2006 12:37:03 -0700 (PDT)

I have not been able to successfully use PMEMD in
amber8 with the options ntr=1 and nmropt=1 (when
ntr=0, the simulation runs fine). So I am attempting
to compile PMEMD from AMBER9 and hoping that this
issue has been resolved. I have successfully compiled
AMBER 9 in parallel, but I get an error when I attempt
to compile pmemd (see below). The configure option
thatI use is the following:

./configure linux_p4 ifort mpich2

I would be grateful for any assistance on this matter.


erfcfun.fpp erfcfun.f90
ifort -c -auto -tpp7 -xN -ip -O3 erfcfun.f90
ifort -o pmemd gbl_constants.o gbl_datatypes.o
state_info.o file_io_dat.o parallel_dat.o
mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o
inpcrd_dat.o dynamics_dat.o img.o parallel.o
pme_direct.o pme_recip.o pme_fft.o fft1d.o bspline.o
pme_force.o pbc.o nb_pairlist.o cit.o dynamics.o
bonds.o angles.o dihedrals.o runmd.o loadbal.o shake.o
runmin.o constraints.o axis_optimize.o gb_ene.o
veclib.o gb_force.o timers.o pmemd_lib.o runfiles.o
file_io.o bintraj.o pmemd_clib.o pmemd.o random.o
degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o
master_setup.o alltasks_setup.o pme_setup.o
ene_frc_splines.o nextprmtop_section.o
-L/opt/mpich2_icc/lib -lmpich -lrt -luuid -lpthread
-limf -lsvml -Wl,-rpath=/opt/intel/lib
ld: cannot find -luuid
make[1]: *** [pmemd] Error 1
make[1]: Leaving directory `/opt/amber9/src/pmemd/src'
make: *** [install] Error 2

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Received on Tue May 09 2006 - 17:06:51 PDT
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