AMBER Archive (2009)

Subject: Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala

From: Wallace Kunin (kunin_at_marshall.edu)
Date: Mon Nov 09 2009 - 16:05:32 CST

g++ is version 4.4.1

I applied Mark Williamson's fix in the
./src/gleap/mortsrc/common/fortran.cpp file.

I did make -f makefile_at clean using gfortran and it went all the way
through but it had a few errors on the way. When I tested it was cut short
by an error. Here are my outputs.

I also uninstalled g77 completely.

COMPILE

kunin_at_admin-laptop:~/amber10/src$ make -f Makefile_at clean
(cd ucpp-1.3 && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/ucpp-1.3'
Makefile:35: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
rm -f *.o ucpp core
make[1]: Leaving directory `/home/kunin/amber10/src/ucpp-1.3'
(cd byacc && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/byacc'
make[1]: Leaving directory `/home/kunin/amber10/src/byacc'
(cd cifparse && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/cifparse'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
rm -f *.o cifparse.a y.output
rm -f lex.cif.c cifp.tab.c cifp.tab.h
make[1]: Leaving directory `/home/kunin/amber10/src/cifparse'
(cd nab && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/nab'
rm -f *.o nab nab2c libnab.a checkexpr.c
rm -f y.tab.c y.tab.h
(cd ../semantics; make clean )
make[2]: Entering directory `/home/kunin/amber10/src/semantics'
/bin/rm parse *.html
/bin/rm: cannot remove `parse': No such file or directory
/bin/rm: cannot remove `*.html': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/home/kunin/amber10/src/semantics'
make[1]: Leaving directory `/home/kunin/amber10/src/nab'
(cd nss && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/nss'
Makefile:17: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
rm -f \
    *.o \
    libsym.a \
    matextract \
    matgen \
    matmerge \
    matmul \
    transform \
    tss_init \
    tss_main \
    tss_next \
    ma \
    mg_2_fold \
    mg_3_fold \
    mg_4_fold \
    mg_5_fold \
    mg_6_fold \
    mg_N_fold \
    mg_cube \
    mg_dihedral \
    mg_helix \
    mg_ico \
    mg_octa \
    mg_orient \
    mg_orient2 \
    mg_rand \
    mg_rotate \
    mg_tetra \
    mg_translate \
    mm \
    mr \
    mw \
    mx \
    ron
make[1]: Leaving directory `/home/kunin/amber10/src/nss'
(cd leap && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/leap'
cd src/Wc; make clean
make[2]: Entering directory `/home/kunin/amber10/src/leap/src/Wc'
Makefile:10: warning: overriding commands for target `.c.o'
../../../config.h:99: warning: ignoring old commands for target `.c.o'
/bin/rm *.o *.a
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `*.a': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/home/kunin/amber10/src/leap/src/Wc'
cd src/Xmu; make clean
make[2]: Entering directory `/home/kunin/amber10/src/leap/src/Xmu'
Makefile:122: warning: overriding commands for target `.c.o'
../../../config.h:99: warning: ignoring old commands for target `.c.o'
/bin/rm *.o *.a
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `*.a': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/home/kunin/amber10/src/leap/src/Xmu'
cd src/Xpm; make clean
make[2]: Entering directory `/home/kunin/amber10/src/leap/src/Xpm'
Makefile:10: warning: overriding commands for target `.c.o'
../../../config.h:99: warning: ignoring old commands for target `.c.o'
/bin/rm *.o *.a
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `*.a': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/home/kunin/amber10/src/leap/src/Xpm'
cd src/Xraw; make clean
make[2]: Entering directory `/home/kunin/amber10/src/leap/src/Xraw'
Makefile:10: warning: overriding commands for target `.c.o'
../../../config.h:99: warning: ignoring old commands for target `.c.o'
/bin/rm *.o *.a
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `*.a': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/home/kunin/amber10/src/leap/src/Xraw'
cd src/leap; make clean
make[2]: Entering directory `/home/kunin/amber10/src/leap/src/leap'
/bin/rm *.o xaLeap teLeap utilMakeHelp utilDescribeTopology utilCrd2Off
mol2_to_off utilConvertWaterBox utilLib2Pdb *\~
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `xaLeap': No such file or directory
/bin/rm: cannot remove `teLeap': No such file or directory
/bin/rm: cannot remove `utilMakeHelp': No such file or directory
/bin/rm: cannot remove `utilDescribeTopology': No such file or directory
/bin/rm: cannot remove `utilCrd2Off': No such file or directory
/bin/rm: cannot remove `mol2_to_off': No such file or directory
/bin/rm: cannot remove `utilConvertWaterBox': No such file or directory
/bin/rm: cannot remove `utilLib2Pdb': No such file or directory
/bin/rm: cannot remove `*~': No such file or directory
make[2]: [clean] Error 1 (ignored)
/bin/rm XaLeap_wcl
/bin/rm: cannot remove `XaLeap_wcl': No such file or directory
make[2]: [clean] Error 1 (ignored)
/bin/rm *.gprof
/bin/rm: cannot remove `*.gprof': No such file or directory
make[2]: [clean] Error 1 (ignored)
/bin/rm helptext.c
/bin/rm: cannot remove `helptext.c': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/home/kunin/amber10/src/leap/src/leap'
make[1]: Leaving directory `/home/kunin/amber10/src/leap'
(cd gleap && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/gleap'
cd freelib; make clean
make[2]: Entering directory `/home/kunin/amber10/src/gleap/freelib'
cd readline; make clean
make[3]: Entering directory `/home/kunin/amber10/src/gleap/freelib/readline'
Makefile:134: warning: overriding commands for target `.c.o'
../../../config.h:99: warning: ignoring old commands for target `.c.o'
/bin/rm *.o
/bin/rm: cannot remove `*.o': No such file or directory
make[3]: [clean] Error 1 (ignored)
make[3]: Leaving directory `/home/kunin/amber10/src/gleap/freelib/readline'
make[2]: Leaving directory `/home/kunin/amber10/src/gleap/freelib'
cd mortsrc; make clean
make[2]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc'
cd common;make clean
make[3]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc/common'
rm -f qmake_image_collection.cpp
rm -f numvec.o pertab.o fortran.o hashcode.o algorithm.o
rm -f *~ core *.core
make[3]: Leaving directory `/home/kunin/amber10/src/gleap/mortsrc/common'
cd object;make clean
make[3]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc/object'
rm -f qmake_image_collection.cpp
rm -f adjacency.o addhs.o atomexpr.o atomfun.o bondfun.o atomvec.o
component.o database.o entity.o finder.o fixbo.o molecule.o molfun.o moref.o
moiter.o namemap.o parmfun.o resdfun.o ring.o subst.o
rm -f *~ core *.core
make[3]: Leaving directory `/home/kunin/amber10/src/gleap/mortsrc/object'
cd ambfmt;make clean
make[3]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc/ambfmt'
rm -f qmake_image_collection.cpp
rm -f ambfrc-amber.o ambfrc-amoeba.o amboff.o chain.o exclude.o extent.o
les.o parm.o parmset.o prep.o prmtop-amoeba.o prmtop.o
rm -f *~ core *.core
make[3]: Leaving directory `/home/kunin/amber10/src/gleap/mortsrc/ambfmt'
cd atmask;make clean
make[3]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc/atmask'
rm -f qmake_image_collection.cpp
rm -f atom.o condition.o dist.o logic.o mask.o paren.o resd.o
rm -f *~ core *.core
make[3]: Leaving directory `/home/kunin/amber10/src/gleap/mortsrc/atmask'
cd capbox;make clean
make[3]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc/capbox'
rm -f qmake_image_collection.cpp
rm -f addions.o octree.o shaper.o solvate.o
rm -f *~ core *.core
make[3]: Leaving directory `/home/kunin/amber10/src/gleap/mortsrc/capbox'
cd guilib;make clean
make[3]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc/guilib'
rm -f qmake_image_collection.cpp
rm -f command.o console.o control.o grammar.o leaplog.o mainwin.o leaplog.o
libguilib.a
rm -f *~ core *.core
make[3]: Leaving directory `/home/kunin/amber10/src/gleap/mortsrc/guilib'
cd format;make clean
make[3]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc/format'
rm -f qmake_image_collection.cpp
rm -f ambfrc.o amboff.o format.o mdlfmt.o pdbent.o prmtop.o smarts.o
tripos.o
rm -f *~ core *.core
make[3]: Leaving directory `/home/kunin/amber10/src/gleap/mortsrc/format'
cd smarts;make clean
make[3]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc/smarts'
rm -f qmake_image_collection.cpp
rm -f parse.o reader.o status.o
rm -f *~ core *.core
make[3]: Leaving directory `/home/kunin/amber10/src/gleap/mortsrc/smarts'
cd tripos;make clean
make[3]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc/tripos'
rm -f qmake_image_collection.cpp
rm -f atom.o bond.o head.o resd.o sect.o
rm -f *~ core *.core
make[3]: Leaving directory `/home/kunin/amber10/src/gleap/mortsrc/tripos'
cd pdbent;make clean
make[3]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc/pdbent'
rm -f qmake_image_collection.cpp
rm -f atom.o build.o second.o
rm -f *~ core *.core
make[3]: Leaving directory `/home/kunin/amber10/src/gleap/mortsrc/pdbent'
cd nablib;make clean
make[3]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc/nablib'
Makefile:4: warning: overriding commands for target `.c.o'
../../../config.h:99: warning: ignoring old commands for target `.c.o'
/bin/rm -f *.o libnab.a lex.mm_options.c
make[3]: Leaving directory `/home/kunin/amber10/src/gleap/mortsrc/nablib'
rm -f libmort.a
rm -f ambfmt/ambfrc-amber.o ambfmt/ambfrc-amoeba.o ambfmt/amboff.o
ambfmt/chain.o ambfmt/exclude.o ambfmt/extent.o
ambfmt/les.o ambfmt/parm.o ambfmt/parmset.o
ambfmt/prmtop-amoeba.o ambfmt/prmtop.o ambfmt/prep.o
atmask/atom.o atmask/condition.o atmask/dist.o
atmask/logic.o atmask/mask.o atmask/paren.o atmask/resd.o
capbox/addions.o capbox/octree.o capbox/solvate.o
capbox/shaper.o common/numvec.o common/pertab.o
common/fortran.o common/hashcode.o common/algorithm.o
enefrc/bonding.o enefrc/ctrlparm.o enefrc/nonbond-egb.o
enefrc/nonbond-lst.o enefrc/nonbond-pbc.o format/ambfrc.o
format/amboff.o format/format.o format/mdlfmt.o
format/pdbent.o format/prmtop.o format/smarts.o
format/tripos.o guilib/command.o guilib/console.o
guilib/control.o guilib/mainwin.o guilib/grammar.o
guilib/leaplog.o object/adjacency.o object/entity.o
object/finder.o object/atomexpr.o object/atomfun.o
object/bondfun.o object/atomvec.o object/component.o
object/database.o object/moiter.o object/molecule.o
object/molfun.o object/parmfun.o object/moref.o
object/resdfun.o object/ring.o object/subst.o
object/namemap.o object/fixbo.o object/addhs.o
pdbent/atom.o pdbent/build.o pdbent/second.o
smarts/parse.o smarts/reader.o smarts/status.o
tripos/atom.o tripos/bond.o tripos/head.o
tripos/resd.o tripos/sect.o nablib/binpos.o
nablib/conjgrad.o nablib/memutil.o nablib/prm.o
nablib/rand2.o nablib/sff.o nablib/time.o
nablib/traceback.o nablib/boundsutil.o nablib/molsurf.o
make[2]: Leaving directory `/home/kunin/amber10/src/gleap/mortsrc'
cd plugins; make clean
make[2]: Entering directory `/home/kunin/amber10/src/gleap/plugins'
rm -f qmake_image_collection.cpp
rm -f add.o addmap.o addions.o bond.o center.o charge.o copy.o create.o
desc.o delete.o energy.o geom.o help.o impose.o list.o loadcrd.o loadfrc.o
loadmol2.o loadoff.o loadpdb.o loadprep.o loadsdf.o measure.o merge.o
moloper.o savemol2.o saveoff.o savepdb.o saveprm.o savesdf.o set.o shell.o
solvate.o source.o zmatrix.o
rm -f *~ core *.core
make[2]: Leaving directory `/home/kunin/amber10/src/gleap/plugins'
cd leapsrc; make clean
make[2]: Entering directory `/home/kunin/amber10/src/gleap/leapsrc'
rm -f qmake_image_collection.cpp
rm -f strmain.o strbuff.o plugins.o
rm -f *~ core *.core
make[2]: Leaving directory `/home/kunin/amber10/src/gleap/leapsrc'
cd mortsrc/mortgl; make clean
make[2]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc/mortgl'
rm -f drawing.o glstyle.o glutils.o graphic.o mouse.o ortho.o ribbon.o
rm -f *~ core *.core
make[2]: Leaving directory `/home/kunin/amber10/src/gleap/mortsrc/mortgl'
cd leapsrc/widget; make clean
make[2]: Entering directory `/home/kunin/amber10/src/gleap/leapsrc/widget'
rm -f main.o glarea.o status.o mainwin.o editbar.o fixbond.o fastbld.o
addhydr.o setpchg.o parmchk.o solvate.o addions.o plugins.o ffparam.o
gconsole.o basicdlg.o shidedlg.o labeldlg.o strcombo.o strradio.o mskcombo.o
solradio.o
rm -f *~ core *.core
make[2]: Leaving directory `/home/kunin/amber10/src/gleap/leapsrc/widget'
make[1]: Leaving directory `/home/kunin/amber10/src/gleap'
(cd carpack && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/carpack'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
/bin/rm -f *.o arpack.a
make[1]: Leaving directory `/home/kunin/amber10/src/carpack'
(cd cblas && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/cblas'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
/bin/rm -f *.o blas.a
make[1]: Leaving directory `/home/kunin/amber10/src/cblas'
(cd clapack && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/clapack'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
/bin/rm -f *.o lapack.a
make[1]: Leaving directory `/home/kunin/amber10/src/clapack'
(cd f2c && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/f2c'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
/bin/rm -f *.o f2c.a
make[1]: Leaving directory `/home/kunin/amber10/src/f2c'
(cd c9x-complex && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/c9x-complex'
rm -f *.o
make[1]: Leaving directory `/home/kunin/amber10/src/c9x-complex'
(cd antechamber && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/antechamber'
Makefile:219: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
rm -f *.o am1bcc acdoctor antechamber atomtype bondtype charmmgen database
espgen parmcal parmchk prepgen residuegen respgen translate top2mol2
test-penalties test-int-part test-combination
make[1]: Leaving directory `/home/kunin/amber10/src/antechamber'
(cd mopac6/src && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/mopac6/src'
rm -f 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
make[1]: Leaving directory `/home/kunin/amber10/src/mopac6/src'
(cd resp && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/resp'
rm -f lapack.o resp.o
make[1]: Leaving directory `/home/kunin/amber10/src/resp'
(cd ptraj && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/ptraj'
Makefile:24: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
cd pdb; make clean
make[2]: Entering directory `/home/kunin/amber10/src/ptraj/pdb'
rm -f pdbrun.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o ms.o
make[2]: Leaving directory `/home/kunin/amber10/src/ptraj/pdb'
/bin/rm -f 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 rdparm ptraj
make[1]: Leaving directory `/home/kunin/amber10/src/ptraj'
(cd reduce && make clean )
make[1]: Entering directory `/home/kunin/amber10/src/reduce'
cleaning in /toolclasses...
make[2]: Entering directory `/home/kunin/amber10/src/reduce/toolclasses'
make[2]: Leaving directory `/home/kunin/amber10/src/reduce/toolclasses'
cleaning in /libpdb...
make[2]: Entering directory `/home/kunin/amber10/src/reduce/libpdb'
make[2]: Leaving directory `/home/kunin/amber10/src/reduce/libpdb'
cleaning in /reduce_src...
make[2]: Entering directory `/home/kunin/amber10/src/reduce/reduce_src'
make[2]: Leaving directory `/home/kunin/amber10/src/reduce/reduce_src'
make[1]: Leaving directory `/home/kunin/amber10/src/reduce'
(cd netcdf/src && make clean)
make[1]: Entering directory `/home/kunin/amber10/src/netcdf/src'
Making clean in examples
make[2]: Entering directory `/home/kunin/amber10/src/netcdf/src/examples'
Making clean in CDL
make[3]: Entering directory
`/home/kunin/amber10/src/netcdf/src/examples/CDL'
test -z "simple_xy.nc sfc_pres_temp.nc pres_temp_4D.nc" || rm -f
simple_xy.nc sfc_pres_temp.nc pres_temp_4D.nc
rm -rf .libs _libs
rm -f *.lo
make[3]: Leaving directory `/home/kunin/amber10/src/netcdf/src/examples/CDL'
Making clean in C
make[3]: Entering directory `/home/kunin/amber10/src/netcdf/src/examples/C'
 rm -f simple_xy_wr simple_xy_wr
 rm -f simple_xy_rd simple_xy_rd
 rm -f sfc_pres_temp_wr sfc_pres_temp_wr
 rm -f sfc_pres_temp_rd sfc_pres_temp_rd
 rm -f pres_temp_4D_wr pres_temp_4D_wr
 rm -f pres_temp_4D_rd pres_temp_4D_rd
test -z "sfc_pres_temp.nc simple_xy.nc pres_temp_4D.nc" || rm -f
sfc_pres_temp.nc simple_xy.nc pres_temp_4D.nc
rm -rf .libs _libs
rm -f *.o
rm -f *.lo
make[3]: Leaving directory `/home/kunin/amber10/src/netcdf/src/examples/C'
Making clean in .
make[3]: Entering directory `/home/kunin/amber10/src/netcdf/src/examples'
rm -rf .libs _libs
rm -f *.lo
make[3]: Leaving directory `/home/kunin/amber10/src/netcdf/src/examples'
make[2]: Leaving directory `/home/kunin/amber10/src/netcdf/src/examples'
Making clean in nc_test
make[2]: Entering directory `/home/kunin/amber10/src/netcdf/src/nc_test'
 rm -f tst_small tst_small
 rm -f nc_test nc_test
test -z "nc_test_classic.nc nc_test_64bit.nc nc_test_netcdf4.nc
tst_small_classic.nc tst_small_64bit.nc tst_small_netcdf4_classic.nc
tst_small_netcdf4.nc " || rm -f nc_test_classic.nc nc_test_64bit.nc
nc_test_netcdf4.nc tst_small_classic.nc tst_small_64bit.nc
tst_small_netcdf4_classic.nc tst_small_netcdf4.nc
rm -rf .libs _libs
rm -f *.o
rm -f *.lo
make[2]: Leaving directory `/home/kunin/amber10/src/netcdf/src/nc_test'
Making clean in ncdump
make[2]: Entering directory `/home/kunin/amber10/src/netcdf/src/ncdump'
 rm -f ncdump ncdump
 rm -f rewrite-scalar rewrite-scalar
 rm -f ctest ctest
 rm -f ctest64 ctest64
 rm -f ncdump ncdump
test -z "test0.nc tst_small.nc tst_small.cdl test1.cdl test1.nc test2.cdl
ctest1.cdl ctest.c ctest64.c ctest0.nc ctest0_64.nc c1.cdl ctest1_64.cdl
c0.nc tst_solar_1.cdl small.nc small2.nc c0tmp.nc " || rm -f test0.nc
tst_small.nc tst_small.cdl test1.cdl test1.nc test2.cdl ctest1.cdl ctest.c
ctest64.c ctest0.nc ctest0_64.nc c1.cdl ctest1_64.cdl c0.nc tst_solar_1.cdl
small.nc small2.nc c0tmp.nc
rm -rf .libs _libs
rm -f *.o
rm -f *.lo
make[2]: Leaving directory `/home/kunin/amber10/src/netcdf/src/ncdump'
Making clean in ncgen
make[2]: Entering directory `/home/kunin/amber10/src/netcdf/src/ncgen'
 rm -f ncgen ncgen
test -z "c0.nc c0_64.nc " || rm -f c0.nc c0_64.nc
rm -rf .libs _libs
rm -f *.o
rm -f *.lo
make[2]: Leaving directory `/home/kunin/amber10/src/netcdf/src/ncgen'
Making clean in nctest
make[2]: Entering directory `/home/kunin/amber10/src/netcdf/src/nctest'
 rm -f nctest nctest
test -z "nctest_classic.nc nctest_64bit_offset.nc nctest_netcdf4.nc test2.nc"
|| rm -f nctest_classic.nc nctest_64bit_offset.nc nctest_netcdf4.nc test2.nc
rm -rf .libs _libs
rm -f *.o
rm -f *.lo
make[2]: Leaving directory `/home/kunin/amber10/src/netcdf/src/nctest'
Making clean in libsrc
make[2]: Entering directory `/home/kunin/amber10/src/netcdf/src/libsrc'
 rm -f t_nc t_nc
test -z "test.nc" || rm -f test.nc
test -z "libnetcdf.la" || rm -f libnetcdf.la
rm -f "./so_locations"
rm -rf .libs _libs
test -z "libnetcdf2.la " || rm -f libnetcdf2.la
rm -f "./so_locations"
rm -f *.o
rm -f *.lo
make[2]: Leaving directory `/home/kunin/amber10/src/netcdf/src/libsrc'
Making clean in .
make[2]: Entering directory `/home/kunin/amber10/src/netcdf/src'
rm -rf .libs _libs
rm -f *.lo
make[2]: Leaving directory `/home/kunin/amber10/src/netcdf/src'
make[1]: Leaving directory `/home/kunin/amber10/src/netcdf/src'
(cd netcdf/lib && rm -f *.a *.la)
(cd netcdf/include && rm -f *.mod netcdf.*)
(cd netcdf/bin && rm -f *)

TESTS

kunin_at_admin-laptop:~/amber10/src$ cd ../test
kunin_at_admin-laptop:~/amber10/test$ make -f Makefile_at test
( cd nab; make test )
make[1]: Entering directory `/home/kunin/amber10/test/nab'
=====================================================
Running test to make dna duplex:

    PASSED
=====================================================
Running Reflexive test:

    PASSED
=====================================================
Running test of hashed arrays:

    PASSED
=====================================================
Running test to compute chemical shifts
   (This tests many parts of the compiler and libraries)

    PASSED

=====================================================
Running test to do simple minimization
   (This tests the molecular mechanics interface)

    PASSED

=====================================================
Running test to do simple minimization with shake
   (This tests the molecular mechanics interface)

    PASSED

=====================================================
Running test to do simple minimization
   (This tests the generalized Born implementation)

    PASSED

=====================================================
Running test to do simple minimization
   (This tests the LCPO surface area)

    PASSED

=====================================================
Running test to do simple minimization
   (This tests the ao generalized Born implementation)

    PASSED

=====================================================
Running test to do molecular dynamics with rattle

    PASSED

=====================================================
Running test of fibre-diffraction module

    PASSED

=====================================================
Running test of randomized embedding

1c1
< radius of gyration: 7.340 

---
> radius of gyration:    7.196
   FAILED (OK if gyration radius is about 7 or 8)
=====================================================
Running test to compute NAB energy of 3dfr minus waters.

Compare the NAB energy with the previously computed Amber energy:
Amber8 total energy is 5184.0880
   NAB total energy is 5184.0880

    PASSED
=====================================================
Running test to create Amber force-field description

    PASSED

=====================================================
checking the prmtop file:

    PASSED
=====================================================
Running test to compute GB Newton-Raphson and normal modes:

    PASSED

=====================================================
Running test to compute non-GB Newton-Raphson and normal modes:

    PASSED

=====================================================
Running test to create a simple mmCIF file

    PASSED
=====================================================
Running test to do simple xmin minimization

    PASSED

=====================================================
Running test to compute GB normal modes using DSYEVD:

    PASSED

=====================================================
Running test to compute GB normal modes using DSAUPD:

    PASSED

=====================================================
Running test to compute Langevin modes:

    PASSED

=====================================================
Running test to do simple lmod optimization

1c1
< Glob. min. E         =     -122.793 kcal/mol
---
> Glob. min. E         =     -122.994 kcal/mol
   FAILED (probably OK if energy is -115 to -125)

=====================================================
Running test to do simple minimization
   (This tests the generalized Born implementation)

    PASSED

=====================================================
make[1]: Leaving directory `/home/kunin/amber10/test/nab'
cd ptraj_rmsa && ./Run.rms
diffing rms.dat.save with rms.dat
PASSED
==============================================================
cd ptraj_rms && ./Run.rms

ptraj: test rms and 2drms commands
diffing rms_fit.dat.save with rms_fit.dat
PASSED
==============================================================
diffing rms_nofit.dat.save with rms_nofit.dat
PASSED
==============================================================
diffing rms2d.ps.save with rms2d.ps
PASSED
==============================================================
cd ptraj_matrix && ./Run.matrix

ptraj: analyze fluctuation matrices
diffing 1rrb_vac_distmat.dat.save with 1rrb_vac_distmat.dat
PASSED
==============================================================
diffing 1rrb_vac_mwcovarmat_evecs.dat.save with
1rrb_vac_mwcovarmat_evecs.dat
PASSED
==============================================================
diffing 1rrb_vac_distcovarmat_evecs.dat.save with
1rrb_vac_distcovarmat_evecs.dat
PASSED
==============================================================
cd antechamber/top2mol2 && ./Run.top2mol2
diffing sustiva.mol2.save with sustiva.mol2
PASSED
==============================================================
diffing dna.mol2.save with dna.mol2
PASSED
==============================================================
diffing dna_wat.mol2.save with dna_wat.mol2
PASSED
==============================================================
diffing aa.mol2.save with aa.mol2
PASSED
==============================================================
cd antechamber/database && ./Run.database
diffing total.frcmod.save with total.frcmod
PASSED
==============================================================
diffing total.prepi.save with total.prepi
PASSED
==============================================================
cd antechamber/bondtype && ./Run.bondtype
diffing ABAKOE.prepi.save with ABAKOE.prepi
PASSED
==============================================================
diffing PFPHHG02.prepi.save with PFPHHG02.prepi
PASSED
==============================================================
diffing fluorescein2.mol2.save with fluorescein2.mol2
PASSED
==============================================================
diffing fluorescein_f2.mol2.save with fluorescein_f2.mol2
PASSED
==============================================================
cd antechamber/c60 && ./Run.c60
diffing buckyball.mol2.save with buckyball.mol2
PASSED
==============================================================
diffing buckyball.gzmat.save with buckyball.gzmat
PASSED
==============================================================
diffing buckyball.jcrt.save with buckyball.jcrt
PASSED
==============================================================
diffing buckyball.prepi.save with buckyball.prepi
PASSED
==============================================================
diffing buckyball.ac.save with buckyball.ac
PASSED
==============================================================
cd antechamber/charmm && ./Run.charmm
diffing ala2.inp.save with ala2.inp
PASSED
==============================================================
diffing ala2.rtf.save with ala2.rtf
PASSED
==============================================================
diffing ala2.prm.save with ala2.prm
PASSED
==============================================================
diffing ala2_charmm.mol2.save with ala2_charmm.mol2
PASSED
==============================================================
cd antechamber/chemokine && ./Run.1b2t
diffing 1b2t.mol2.save with 1b2t.mol2
PASSED
==============================================================
diffing 1b2t.ac.save with 1b2t.ac
PASSED
==============================================================
cd antechamber/tp && ./Run.tp
  ./Run.tp:  Program error
make: *** [test.antechamber.hasG77] Error 1
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