cd /mnt/c/Users/Alen/Documents/Research/amber18//AmberTools/src && make install make[1]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src' Starting installation of AmberTools19 serial at Tue Nov 5 16:40:16 EST 2019. (cd ucpp-1.3 && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/ucpp-1.3' [UCPP] CC ucpp mv ucpp /mnt/c/Users/Alen/Documents/Research/amber18//bin make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/ucpp-1.3' (cd arpack && make install ); make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/arpack' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/arpack' (cd lapack && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lapack' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lapack' (cd blas && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/blas' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/blas' (cd c9x-complex && make skip ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/c9x-complex' using built-in (C99) complex.h functionality make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/c9x-complex' (cd pbsa && make -j1 install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/pbsa' [PBSA] FC pbsa.F90 [PBSA] FC np_force.F90 [PBSA] FC pb_read.F90 [PBSA] FC pb_write.F90 [PBSA] FC force.F90 [PBSA] FC pb_init.F90 [PBSA] FC pb_p3m.F90 [PBSA] FC pb_anaiim.F90 [PBSA] FC pb_augdrv.F90 [PBSA] FC pb_fdfrc.F90 [PBSA] FC pb_crgview.F90 Always rebuild [ pb_lsolver.o pb_fddrv.o [ cuda_pb.o kLinearSolvers.o cuda_LinearSolvers.o cusparse_LinearSolvers.o cusp_LinearSolvers.o ]] to make predefined macros effective [PBSA] FC pb_lsolver.F90 [PBSA] FC pb_fddrv.F90 [PBSA] FC pb_bldsys.F90 [PBSA] FC pb_direct.F90 [PBSA] FC pb_list.F90 [PBSA] FC irre31.F90 [PBSA] FC irre32.F90 [PBSA] FC jumps.F90 [PBSA] FC pb_chkfrc.F90 [PBSA] FC interpX.F90 [PBSA] FC rdpqr.F90 cd ../lib && make nxtsec.o random.o make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' make[3]: 'nxtsec.o' is up to date. make[3]: 'random.o' is up to date. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' cd ../lapack && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lapack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lapack' cd ../blas && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/blas' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/blas' cd ../arpack && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/arpack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/arpack' [PBSA] FC pbsa /bin/mv pbsa /mnt/c/Users/Alen/Documents/Research/amber18//bin make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/pbsa' (cd gbnsr6 && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/gbnsr6' cd ../lib && make nxtsec.o random.o make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' make[3]: 'nxtsec.o' is up to date. make[3]: 'random.o' is up to date. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' cd ../lapack && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lapack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lapack' cd ../blas && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/blas' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/blas' cd ../arpack && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/arpack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/arpack' [GBNSR6] FC gbnsr6 /bin/mv gbnsr6 /mnt/c/Users/Alen/Documents/Research/amber18//bin make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/gbnsr6' (cd cifparse && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cifparse' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cifparse' (cd antechamber && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/antechamber' [ANTECHAMBER] CC am1bcc [ANTECHAMBER] CC antechamber [ANTECHAMBER] CC atomtype [ANTECHAMBER] CC bondtype [ANTECHAMBER] CC espgen [ANTECHAMBER] CC parmchk2 [ANTECHAMBER] CC prepgen [ANTECHAMBER] CC residuegen [ANTECHAMBER] CC respgen SFX= BINDIR=/mnt/c/Users/Alen/Documents/Research/amber18//bin sh patch.sh make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/antechamber' (cd sqm && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/sqm' cd ../lapack; make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lapack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lapack' cd ../blas; make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/blas' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/blas' cd ../arpack && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/arpack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/arpack' cd ../lib; make sys.a make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' make[3]: 'sys.a' is up to date. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' [SQM] FC sqm mv sqm /mnt/c/Users/Alen/Documents/Research/amber18//bin make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/sqm' (cd reduce && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/reduce' installing ./toolclasses... make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/reduce/toolclasses' make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/reduce/toolclasses' installing ./libpdb... make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/reduce/libpdb' make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/reduce/libpdb' installing ./reduce_src... make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/reduce/reduce_src' [REDUCE] CXX reduce mv reduce /mnt/c/Users/Alen/Documents/Research/amber18//bin/to_be_dispatched/ cat ../reduce_template | sed "s/REPLACE_ME/reduce/" > /mnt/c/Users/Alen/Documents/Research/amber18//bin/reduce chmod +x /mnt/c/Users/Alen/Documents/Research/amber18//bin/reduce /bin/rm -f /mnt/c/Users/Alen/Documents/Research/amber18//dat/reduce_wwPDB_het_dict.txt cp /mnt/c/Users/Alen/Documents/Research/amber18//AmberTools/src/reduce/reduce_wwPDB_het_dict.txt /mnt/c/Users/Alen/Documents/Research/amber18//dat/reduce_wwPDB_het_dict.txt make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/reduce/reduce_src' make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/reduce' (if [ = "yes" ]; then \ cd moft && make install;\ fi;\ ) (cd leap && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap' Compiling basic programs cd src/leap && make installteLeap make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap/src/leap' [LEAP] CC teLeap mv teLeap /mnt/c/Users/Alen/Documents/Research/amber18//bin make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap/src/leap' Copying shell script cp tleap /mnt/c/Users/Alen/Documents/Research/amber18//bin/tleap chmod +x /mnt/c/Users/Alen/Documents/Research/amber18//bin/tleap make install_xleap make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap' cd src/Wc && make make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap/src/Wc' make[4]: 'libWcLeap.a' is up to date. make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap/src/Wc' cd src/Xmu && make make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap/src/Xmu' make[4]: 'libXmu.a' is up to date. make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap/src/Xmu' cd src/Xpm && make make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap/src/Xpm' make[4]: 'libXpm.a' is up to date. make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap/src/Xpm' cd src/Xraw && make make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap/src/Xraw' make[4]: 'libXaw.a' is up to date. make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap/src/Xraw' cd src/leap && make install make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap/src/leap' [LEAP] CC teLeap [LEAP] CC xaLeap m4 xaLeap.rm4 > XaLeap_wcl mv teLeap xaLeap /mnt/c/Users/Alen/Documents/Research/amber18//bin mv XaLeap_wcl /mnt/c/Users/Alen/Documents/Research/amber18//dat make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap/src/leap' Copying shell script cp xleap /mnt/c/Users/Alen/Documents/Research/amber18//bin/xleap chmod +x /mnt/c/Users/Alen/Documents/Research/amber18//bin/xleap Copying pixmaps test -d /mnt/c/Users/Alen/Documents/Research/amber18//dat/pixmap || mkdir /mnt/c/Users/Alen/Documents/Research/amber18//dat/pixmap cd pixmap; /bin/cp * /mnt/c/Users/Alen/Documents/Research/amber18//dat/pixmap Finished with the install of LEaP make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap' make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/leap' (cd lib && make install) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' [LIB] FC new2oldparm.o make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' (cd addles && make install) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/addles' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/addles' (cd sander && make serial) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/sander' cd ../sqm && make libsqm make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/sqm' make[3]: Nothing to be done for 'libsqm'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/sqm' test -e qmmm_module.o || touch qmmm_module.o cd ../pbsa && make -j1 libFpbsa.a make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/pbsa' [PBSA] FC pb_fdfrc.F90 [PBSA] AR libFpbsa.a make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/pbsa' test -e poisson_boltzmann.o || touch poisson_boltzmann.o test -e qm2_read_nm_and_alloc.o || touch qm2_read_nm_and_alloc.o test -e qmmm_vsolv_module.o || touch qmmm_vsolv_module.o test -e elementOrbitalIndex.o || touch elementOrbitalIndex.o test -e utilitiesmodule.o || touch utilitiesmodule.o test -e qmmm_nml_module.o || touch qmmm_nml_module.o test -e qmmm_struct_module.o || touch qmmm_struct_module.o make -C ../emil install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/emil' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/emil' cd ../sebomd && make sebomd.a make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/sebomd' make[3]: 'sebomd.a' is up to date. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/sebomd' test -e dispersion_cavity.o || touch dispersion_cavity.o test -e pbtimer_module.o || touch pbtimer_module.o cd ../lib && make sys.a make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' make[3]: 'sys.a' is up to date. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' cd ../blas && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/blas' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/blas' cd ../lapack && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lapack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lapack' cd ../arpack && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/arpack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/arpack' if [ -n "-DRISMSANDER" ]; then \ cd ../rism && make librism; \ fi make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/rism' [RISM] AR librism make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/rism' [SANDER] FC /mnt/c/Users/Alen/Documents/Research/amber18//bin/sander [SANDER] FC /mnt/c/Users/Alen/Documents/Research/amber18//bin/sander.LES [SANDER] FC /mnt/c/Users/Alen/Documents/Research/amber18//lib/libsander.so [SANDER] FC /mnt/c/Users/Alen/Documents/Research/amber18//lib/libsanderles.so cd ../../../test/amd && ln -s -f ../../bin/sander . cd ../../../test/chamber && ln -s -f ../../bin/sander . cd ../../../test/nmropt && ln -s -f ../../bin/sander . cd ../../../test/qmmm2 && ln -s -f ../../bin/sander . cd ../../../test/qmmm_DFTB && ln -s -f ../../bin/sander . cd ../../../test/abfqmmm && ln -s -f ../../bin/sander . cd ../../../test/rism3d && ln -s -f ../../bin/sander . cd ../../../test/sander_pbsa_frc && ln -s -f ../../bin/sander . cd ../../../test/rism3d && ln -s -f ../../bin/sander . make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/sander' (cd nmr_aux && make install) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nmr_aux' cd prepare_input && make clean && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nmr_aux/prepare_input' /bin/rm -f *.o make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nmr_aux/prepare_input' make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nmr_aux/prepare_input' [NMR_AUX] CC makeDIST_RST.c [NMR_AUX] CC makeDIST_RST [NMR_AUX] CC makeANG_RST.c [NMR_AUX] CC makeANG_RST [NMR_AUX] CC nef_to_RST.c [NMR_AUX] CC nef_to_RST make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nmr_aux/prepare_input' cd fantasian && make clean && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nmr_aux/fantasian' /bin/rm -f *.o fantasian make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nmr_aux/fantasian' make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nmr_aux/fantasian' gfortran -DBINTRAJ -DEMIL -c -O0 -fPIC -I/mnt/c/Users/Alen/Documents/Research/amber18//include -I/mnt/c/Users/Alen/Documents/Research/amber18//include -o fantasian.o fantasian.F gfortran -DBINTRAJ -DEMIL -fPIC -I/mnt/c/Users/Alen/Documents/Research/amber18//include -I/mnt/c/Users/Alen/Documents/Research/amber18//include -o fantasian fantasian.o ../../lib/random.o ../../lib/mexit.o mv fantasian /mnt/c/Users/Alen/Documents/Research/amber18//bin make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nmr_aux/fantasian' cp senergy sviol sviol2 /mnt/c/Users/Alen/Documents/Research/amber18//bin make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nmr_aux' (cd nmode && make install) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nmode' cd ../lib && make rfree.o matinv.o nxtsec.o amopen.o rgroup.o make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' make[3]: 'rfree.o' is up to date. make[3]: 'matinv.o' is up to date. make[3]: 'nxtsec.o' is up to date. make[3]: 'amopen.o' is up to date. make[3]: 'rgroup.o' is up to date. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' cd ../lib && make sys.a make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' make[3]: 'sys.a' is up to date. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' cd ../blas && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/blas' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/blas' cd ../lapack && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lapack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lapack' cd ../arpack && make install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/arpack' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/arpack' [NMODE] FC /mnt/c/Users/Alen/Documents/Research/amber18//bin/nmode [NMODE] FC /mnt/c/Users/Alen/Documents/Research/amber18//bin/lmanal make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nmode' make build_cpptraj libcpptraj make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src' (cd cpptraj && make install) make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj' cd src && make install make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj/src' Skipping bundled ARPACK build g++ -o cpptraj SpaceGroup.o Action.o ActionFrameCounter.o ActionList.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AtomType.o AtomTypeArray.o AxisType.o BondSearch.o Box.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o ComplexArray.o Constraints.o Control.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_GenerateAmberRst.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrintData.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_SequenceAlign.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileTypes.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MetaData.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OutputTrajCommon.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o ProgressBar.o ProgressTimer.o PubFFT.o Random.o Range.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o VariableArray.o Vec3.o ViewRst.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o readline/libreadline.a -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -larpack -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -llapack -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -lblas -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -lfftw3 -lgfortran -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -lnetcdf -lbz2 -lz xdrfile/libxdrfile.a mv cpptraj "/mnt/c/Users/Alen/Documents/Research/amber18//bin" make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj/src' make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj' (cd cpptraj && make libcpptraj) make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj' cd src && make libcpptraj make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj/src' Skipping bundled ARPACK build g++ -shared -o "/mnt/c/Users/Alen/Documents/Research/amber18//lib"/libcpptraj.so SpaceGroup.o Action.o ActionFrameCounter.o ActionList.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AtomType.o AtomTypeArray.o AxisType.o BondSearch.o Box.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o ComplexArray.o Constraints.o Control.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_GenerateAmberRst.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrintData.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_SequenceAlign.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileTypes.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MetaData.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OutputTrajCommon.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o ProgressBar.o ProgressTimer.o PubFFT.o Random.o Range.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o VariableArray.o Vec3.o ViewRst.o molsurf.o Action_Esander.LIBCPPTRAJ.o Command.LIBCPPTRAJ.o Cpptraj.LIBCPPTRAJ.o Energy_Sander.LIBCPPTRAJ.o ReadLine.LIBCPPTRAJ.o -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -larpack -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -llapack -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -lblas -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -lfftw3 -lgfortran -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -lnetcdf -lbz2 -lz xdrfile/libxdrfile.a make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj/src' make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj' make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src' (cd ambpdb && make install) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/ambpdb' [AMBPDB] CXX ambpdb mv ambpdb /mnt/c/Users/Alen/Documents/Research/amber18//bin make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/ambpdb' (cd sff && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/sff' cd ../rism && \ make amber_rism_interface.NAB.o make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/rism' make[3]: 'amber_rism_interface.NAB.o' is up to date. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/rism' [SFF] AR libsff [SFF] CC hcp_getpdb.c make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/sff' (cd pbsa && make -j1 libinstall ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/pbsa' [PBSA] FC decomp.F90 [PBSA] FC pb_force.F90 [PBSA] FC pb_iimdrv.F90 [PBSA] FC pb_nhadrv.F90 [PBSA] FC pb_fdfrc.F90 cd ../lib && make nxtsec.o random.o make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' make[3]: 'nxtsec.o' is up to date. make[3]: 'random.o' is up to date. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' [PBSA] AR libpbsa.a /bin/mv libpbsa.a /mnt/c/Users/Alen/Documents/Research/amber18//lib make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/pbsa' (cd rism && make yes ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/rism' [RISM] AR librism [RISM] FC rism1d [RISM] FC rism3d.thermo [RISM] FC rism3d.orave [RISM] FC volslice /bin/mv rism1d rism3d.thermo rism3d.orave \ /mnt/c/Users/Alen/Documents/Research/amber18//bin make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/rism' (cd nab && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nab' [NAB] CC /mnt/c/Users/Alen/Documents/Research/amber18//bin/nab [NAB] NAB fd_helix.nab [NAB] NAB bdna.nab [NAB] NAB dg_helix.nab [NAB] NAB getchivol.nab [NAB] NAB getseq_from_pdb.nab [NAB] NAB getxyz_from_pdb.nab [NAB] NAB getpdb_prm.nab [NAB] NAB linkprot.nab [NAB] NAB link_na.nab [NAB] NAB na_anal.nab [NAB] NAB setboundsfromdb.nab [NAB] NAB setchiplane.nab [NAB] NAB wc_basepair.nab [NAB] NAB wc_complement.nab [NAB] NAB wc_helix.nab [NAB] CC libnab.a make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nab' (cd etc && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/etc' [ETC] CC elsize [ETC] NAB molsurf [ETC] FC resp [ETC] FC tinker_to_amber cd ../lib; make nxtsec.o make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' make[3]: 'nxtsec.o' is up to date. make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/lib' [ETC] FC new_crd_to_dyn [ETC] FC new_to_old_crd [ETC] FC fix_new_inpcrd_vel /bin/mv elsize molsurf resp tinker_to_amber new_crd_to_dyn new_to_old_crd fix_new_inpcrd_vel /mnt/c/Users/Alen/Documents/Research/amber18//bin /bin/cp process_mdout.perl process_minout.perl mdout2pymbar.pl /mnt/c/Users/Alen/Documents/Research/amber18//bin /bin/cp sgldinfo.sh sgldwt.sh /mnt/c/Users/Alen/Documents/Research/amber18//bin make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/etc' (if [ yes = "yes" ]; then \ cd rism && make rism3d.snglpnt; \ fi;\ ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/rism' [RISM] CC rism3d.snglpnt make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/rism' (cd mdgx && make yes ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/mdgx' [MDGX] CC /mnt/c/Users/Alen/Documents/Research/amber18//lib/libmdgx.so make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/mdgx' (cd xtalutil && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/xtalutil' [XTALUTIL] CC AddToBox [XTALUTIL] CC ChBox [XTALUTIL] CC PropPDB [XTALUTIL] CC UnitCell [XTALUTIL] CC CheckMD mv AddToBox ChBox PropPDB UnitCell CheckMD /mnt/c/Users/Alen/Documents/Research/amber18//bin make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/xtalutil' (cd saxs && make install ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/saxs' [SAXS] CXX saxs_rism [SAXS] CXX saxs_md [SAXS] CXX libsaxs_rism.so [SAXS] CXX libsaxs_md.so make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/saxs' (cd mm_pbsa && make install) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/mm_pbsa' cp mm_pbsa.pl mm_pbsa_statistics.pl /mnt/c/Users/Alen/Documents/Research/amber18//bin cp *.pm /mnt/c/Users/Alen/Documents/Research/amber18//lib/perl/mm_pbsa/ make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/mm_pbsa' (cd FEW && make install) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW' gcc miscellaneous/draw_membrane2.c -lm -o miscellaneous/draw_membrane2 AMBER_PREFIX=/mnt/c/Users/Alen/Documents/Research/amber18/ AMBER_SOURCE=/mnt/c/Users/Alen/Documents/Research/amber18/ /bin/sh setup.sh Generating a Unix-style Makefile Writing Makefile for Chemistry::File::VRML Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::3DBuilder Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::Mol Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::Mok Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::File::SMILES Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::File::SMARTS Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::File::PDB Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::Pattern Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::MidasPattern Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::File::MDLMol Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::InternalCoords Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::MacroMol Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::Ring Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::Canonicalize Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::Bond::Find Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::File::SLN Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::FormulaPattern Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::File::Mopac Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::File::XYZ Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::Isotope Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Chemistry::Reaction Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Math::VectorReal Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Statistics::Regression Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Parse::Yapp Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for PerlMol Writing MYMETA.yml and MYMETA.json make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500' Skip blib/lib/PerlMol.pm (unchanged) make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-VRML-0.10' Skip ../blib/lib/Chemistry/File/VRML.pm (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-VRML-0.10' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-3DBuilder-0.10' Skip ../blib/lib/Chemistry/3DBuilder.pm (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-3DBuilder-0.10' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Mol-0.35' Skip ../blib/lib/Chemistry/File/Formula.pm (unchanged) Skip ../blib/lib/Chemistry/Atom.pm (unchanged) Skip ../blib/lib/Chemistry/File/Dumper.pm (unchanged) Skip ../blib/lib/Chemistry/File.pm (unchanged) Skip ../blib/lib/Chemistry/Bond.pm (unchanged) Skip ../blib/lib/Chemistry/Obj.pm (unchanged) Skip ../blib/lib/Chemistry/Tutorial.pod (unchanged) Skip ../blib/lib/Chemistry/Mol.pm (unchanged) Manifying 8 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Mol-0.35' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Mok-0.25' Skip ../blib/lib/Chemistry/Mok.pm (unchanged) cp mok ../blib/script/mok "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- ../blib/script/mok Manifying 1 pod document Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Mok-0.25' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-SMILES-0.44' Skip ../blib/lib/Chemistry/File/write.pl (unchanged) Skip ../blib/lib/Chemistry/File/SMILES.pm (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-SMILES-0.44' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-SMARTS-0.22' Skip ../blib/lib/Chemistry/File/SMARTS.pm (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-SMARTS-0.22' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-PDB-0.21' Skip ../blib/lib/Chemistry/File/PDB.pm (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-PDB-0.21' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Pattern-0.26' Skip ../blib/lib/Chemistry/Pattern/Bond.pm (unchanged) Skip ../blib/lib/Chemistry/Pattern/Atom.pm (unchanged) Skip ../blib/lib/Chemistry/Pattern.pm (unchanged) Manifying 3 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Pattern-0.26' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-MidasPattern-0.11' Skip ../blib/lib/Chemistry/MidasPattern.pm (unchanged) Skip ../blib/lib/Chemistry/File/MidasPattern.pm (unchanged) Manifying 2 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-MidasPattern-0.11' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-MDLMol-0.20' Skip ../blib/lib/Chemistry/File/SDF.pm (unchanged) Skip ../blib/lib/Chemistry/File/MDLMol.pm (unchanged) Manifying 2 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-MDLMol-0.20' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-InternalCoords-0.18' Skip ../blib/lib/Chemistry/InternalCoords/Builder.pm (unchanged) Skip ../blib/lib/Chemistry/InternalCoords.pm (unchanged) Manifying 2 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-InternalCoords-0.18' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-MacroMol-0.06' Skip ../blib/lib/Chemistry/MacroMol.pm (unchanged) Skip ../blib/lib/Chemistry/Domain.pm (unchanged) Manifying 2 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-MacroMol-0.06' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Ring-0.19' Skip ../blib/lib/Chemistry/Ring/Find.pm (unchanged) Skip ../blib/lib/Chemistry/Ring.pm (unchanged) Manifying 2 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Ring-0.19' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Canonicalize-0.10' Skip ../blib/lib/Chemistry/Canonicalize.pm (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Canonicalize-0.10' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Bond-Find-0.21' Skip ../blib/lib/Chemistry/Bond/Find.pm (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Bond-Find-0.21' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-SLN-0.11' Skip ../blib/lib/Chemistry/File/SLN.pm (unchanged) Skip ../blib/lib/Chemistry/File/SLN/Parser.pm (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-SLN-0.11' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-FormulaPattern-0.10' Skip ../blib/lib/Chemistry/File/FormulaPattern.pm (unchanged) Skip ../blib/lib/Chemistry/FormulaPattern.pm (unchanged) Manifying 2 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-FormulaPattern-0.10' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-Mopac-0.15' Skip ../blib/lib/Chemistry/File/Mopac.pm (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-Mopac-0.15' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-XYZ-0.11' Skip ../blib/lib/Chemistry/File/XYZ.pm (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-XYZ-0.11' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Isotope-0.11' Skip ../blib/lib/Chemistry/Isotope.pm (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Isotope-0.11' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Reaction-0.02' Skip ../blib/lib/Chemistry/Reaction.pm (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Reaction-0.02' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Math-VectorReal-1.02' Skip ../blib/lib/Math/synopsis.pl (unchanged) Skip ../blib/lib/Math/matrix_test.pl (unchanged) Skip ../blib/lib/Math/VectorReal.pm (unchanged) Skip ../blib/lib/Math/vector_test.pl (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Math-VectorReal-1.02' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Statistics-Regression-0.15' Skip ../blib/lib/Statistics/Regression.pm (unchanged) Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Statistics-Regression-0.15' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Parse-Yapp-1.05' Skip ../blib/lib/Parse/Yapp/Parse.pm (unchanged) Skip ../blib/lib/Parse/Yapp/Output.pm (unchanged) Skip ../blib/lib/Parse/Yapp/Grammar.pm (unchanged) Skip ../blib/lib/Parse/Yapp/Lalr.pm (unchanged) Skip ../blib/lib/Parse/Yapp/Options.pm (unchanged) Skip ../blib/lib/Parse/Yapp.pm (unchanged) Skip ../blib/lib/Parse/Yapp/Driver.pm (unchanged) cp yapp ../blib/script/yapp "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- ../blib/script/yapp Manifying 1 pod document Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Parse-Yapp-1.05' Manifying 1 pod document make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500' make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-VRML-0.10' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-VRML-0.10' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-3DBuilder-0.10' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-3DBuilder-0.10' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Mol-0.35' Manifying 8 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Mol-0.35' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Mok-0.25' Manifying 1 pod document Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Mok-0.25' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-SMILES-0.44' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-SMILES-0.44' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-SMARTS-0.22' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-SMARTS-0.22' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-PDB-0.21' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-PDB-0.21' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Pattern-0.26' Manifying 3 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Pattern-0.26' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-MidasPattern-0.11' Manifying 2 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-MidasPattern-0.11' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-MDLMol-0.20' Manifying 2 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-MDLMol-0.20' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-InternalCoords-0.18' Manifying 2 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-InternalCoords-0.18' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-MacroMol-0.06' Manifying 2 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-MacroMol-0.06' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Ring-0.19' Manifying 2 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Ring-0.19' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Canonicalize-0.10' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Canonicalize-0.10' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Bond-Find-0.21' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Bond-Find-0.21' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-SLN-0.11' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-SLN-0.11' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-FormulaPattern-0.10' Manifying 2 pod documents make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-FormulaPattern-0.10' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-Mopac-0.15' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-Mopac-0.15' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-XYZ-0.11' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-File-XYZ-0.11' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Isotope-0.11' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Isotope-0.11' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Reaction-0.02' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Chemistry-Reaction-0.02' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Math-VectorReal-1.02' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Math-VectorReal-1.02' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Statistics-Regression-0.15' Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Statistics-Regression-0.15' make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Parse-Yapp-1.05' Manifying 1 pod document Manifying 1 pod document make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500/Parse-Yapp-1.05' Manifying 1 pod document Appending installation info to /mnt/c/Users/Alen/Documents/Research/amber18//lib/perl//lib/x86_64-linux-gnu/perl/5.22.1/perllocal.pod make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW/additional_libs/PerlMol-0.3500' cp -f /mnt/c/Users/Alen/Documents/Research/amber18//AmberTools/src/FEW/FEW.pl /mnt/c/Users/Alen/Documents/Research/amber18//bin make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/FEW' (cd amberlite && make install) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/amberlite' (if [ "no" = "no" ]; then \ /mnt/c/Users/Alen/Documents/Research/amber18//bin/amber.python setup.py install -f --prefix=/mnt/c/Users/Alen/Documents/Research/amber18/ ;\ fi;\ ) running install running build running build_scripts running install_scripts copying build/scripts-2.7/pymdpbsa -> /mnt/c/Users/Alen/Documents/Research/amber18//bin copying build/scripts-2.7/pytleap -> /mnt/c/Users/Alen/Documents/Research/amber18//bin changing mode of /mnt/c/Users/Alen/Documents/Research/amber18//bin/pymdpbsa to 777 changing mode of /mnt/c/Users/Alen/Documents/Research/amber18//bin/pytleap to 777 running install_egg_info Removing /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/AmberLite-16.0-py2.7.egg-info Writing /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/AmberLite-16.0-py2.7.egg-info make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/amberlite' (cd paramfit && make install) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/paramfit' [PARAMFIT] CC paramfit /bin/mv paramfit /mnt/c/Users/Alen/Documents/Research/amber18//bin make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/paramfit' (cd cphstats && make install) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cphstats' [CPHSTATS] CXX cphstats [CPHSTATS] CXX cestats /bin/mv cphstats /mnt/c/Users/Alen/Documents/Research/amber18//bin /bin/mv cestats /mnt/c/Users/Alen/Documents/Research/amber18//bin make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cphstats' (cd nfe-umbrella-slice && make install) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nfe-umbrella-slice' [NFE] CXX nfe-umbrella-slice make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/nfe-umbrella-slice' (if [ "no" = "no" ]; then \ make python_serial ;\ fi;\ ) make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src' (cd parmed && PYTHONPATH=/mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages /mnt/c/Users/Alen/Documents/Research/amber18//bin/amber.python setup.py install -f --prefix=/mnt/c/Users/Alen/Documents/Research/amber18/ > build.log) (cd mmpbsa_py && make install) make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/mmpbsa_py' /mnt/c/Users/Alen/Documents/Research/amber18//bin/amber.python setup.py install -f --prefix=/mnt/c/Users/Alen/Documents/Research/amber18/ --install-scripts=/mnt/c/Users/Alen/Documents/Research/amber18//bin running install running build running build_py running build_scripts running install_lib copying build/lib/MMPBSA_mods/alamdcrd.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/amber_outputs.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/API.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/calculation.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/commandlineparser.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/createinput.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/exceptions.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/fake_mpi.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/findprogs.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/infofile.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/input_parser.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/main.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/make_trajs.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/output_file.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/parm_setup.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/timer.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/utils.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/__init__.py -> /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/alamdcrd.py to alamdcrd.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py to amber_outputs.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/API.py to API.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/calculation.py to calculation.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/commandlineparser.py to commandlineparser.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/createinput.py to createinput.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/exceptions.py to exceptions.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/fake_mpi.py to fake_mpi.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/findprogs.py to findprogs.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/infofile.py to infofile.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/input_parser.py to input_parser.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/main.py to main.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py to make_trajs.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/output_file.py to output_file.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py to parm_setup.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/timer.py to timer.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/utils.py to utils.pyc byte-compiling /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA_mods/__init__.py to __init__.pyc running install_scripts copying build/scripts-2.7/ante-MMPBSA.py -> /mnt/c/Users/Alen/Documents/Research/amber18//bin copying build/scripts-2.7/MMPBSA.py -> /mnt/c/Users/Alen/Documents/Research/amber18//bin changing mode of /mnt/c/Users/Alen/Documents/Research/amber18//bin/ante-MMPBSA.py to 777 changing mode of /mnt/c/Users/Alen/Documents/Research/amber18//bin/MMPBSA.py to 777 running install_egg_info Removing /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA.py-16.0-py2.7.egg-info Writing /mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages/MMPBSA.py-16.0-py2.7.egg-info make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/mmpbsa_py' (cd pysander && make install > build.log) (cd pymsmt && PYTHONPATH=/mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages /mnt/c/Users/Alen/Documents/Research/amber18//bin/amber.python setup.py install -f --prefix=/mnt/c/Users/Alen/Documents/Research/amber18/ > build.log ) make libcpptraj make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src' (cd cpptraj && make libcpptraj) make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj' cd src && make libcpptraj make[5]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj/src' Skipping bundled ARPACK build g++ -shared -o "/mnt/c/Users/Alen/Documents/Research/amber18//lib"/libcpptraj.so SpaceGroup.o Action.o ActionFrameCounter.o ActionList.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AtomType.o AtomTypeArray.o AxisType.o BondSearch.o Box.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o ComplexArray.o Constraints.o Control.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_GenerateAmberRst.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrintData.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_SequenceAlign.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileTypes.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MetaData.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OutputTrajCommon.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o ProgressBar.o ProgressTimer.o PubFFT.o Random.o Range.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o VariableArray.o Vec3.o ViewRst.o molsurf.o Action_Esander.LIBCPPTRAJ.o Command.LIBCPPTRAJ.o Cpptraj.LIBCPPTRAJ.o Energy_Sander.LIBCPPTRAJ.o ReadLine.LIBCPPTRAJ.o -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -larpack -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -llapack -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -lblas -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -lfftw3 -lgfortran -L/mnt/c/Users/Alen/Documents/Research/amber18//lib64 -lnetcdf -lbz2 -lz xdrfile/libxdrfile.a make[5]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj/src' make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj' make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src' (cd pytraj && AMBERHOME=/mnt/c/Users/Alen/Documents/Research/amber18/ AMBER_PREFIX=/mnt/c/Users/Alen/Documents/Research/amber18/ PYTHONPATH=/mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages /mnt/c/Users/Alen/Documents/Research/amber18//bin/amber.python setup.py install -f --prefix=/mnt/c/Users/Alen/Documents/Research/amber18/ --disable-openmp > build.log ) (cd pdb4amber && PYTHONPATH=/mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages /mnt/c/Users/Alen/Documents/Research/amber18//bin/amber.python setup.py install -f --prefix=/mnt/c/Users/Alen/Documents/Research/amber18/ > build.log) (if [ yes = "yes" ]; then \ cd packmol_memgen && PYTHONPATH=/mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages /mnt/c/Users/Alen/Documents/Research/amber18//bin/amber.python setup.py install -f --prefix=/mnt/c/Users/Alen/Documents/Research/amber18/ > build.log && cp packmol_memgen/lib/packmol/packmol packmol_memgen/lib/memembed/bin/memembed /mnt/c/Users/Alen/Documents/Research/amber18//bin; \ else \ cd packmol_memgen && PYTHONPATH=/mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages /mnt/c/Users/Alen/Documents/Research/amber18//bin/amber.python setup.py install -f --prefix=/mnt/c/Users/Alen/Documents/Research/amber18/ --no-memembed > build.log && cp packmol_memgen/lib/packmol/packmol /mnt/c/Users/Alen/Documents/Research/amber18//bin; \ fi;\ ) /mnt/c/Users/Alen/Documents/Research/amber18//bin/amber.python fix_conda_fortran.py make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src' Installation of AmberTools19 serial is complete at Tue Nov 5 16:44:19 EST 2019. make[1]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src' make[1]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/src' Starting installation of Amber18 (serial) at Tue Nov 5 16:44:19 EST 2019. cd pmemd && make install make[2]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/src/pmemd' make -C src/ install make[3]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/src/pmemd/src' gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c gbl_constants.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c gbl_datatypes.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c state_info.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c file_io_dat.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pmemd_lib.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c parallel_dat.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c file_io.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c mdin_ctrl_dat.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c mdin_emil_dat.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c axis_optimize.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c fft1d.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c charmm.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c AmberNetcdf.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nextprmtop_section.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include \ -fno-tree-vectorize -c prmtop_dat.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c mdin_ewald_dat.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c mdin_debugf_dat.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c remd.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c binrestart.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c inpcrd_dat.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c findmask.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c random.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c ti.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c constraints.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c mol_list.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c energy_records.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c ensure_alloc.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c processor.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c timers.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c gbsa.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c gb_ene.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c phmd.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c extra_pnts_nb14.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c prfs.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c dynamics_dat.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c dynamics.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pbc.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c gb_ene_hybrid.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nmr_lib.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nmr_calls.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c angles.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c angles_ub.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c bonds.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c constantph_dat.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c constante_dat.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c cmap.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c dihedrals.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c dihedrals_imp.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c bspline.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c emap.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c gb_parallel.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c img.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pme_recip_dat.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pme_fft_dat.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pme_blk_fft.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pme_slab_fft.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c shake.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c cit.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c bonds_midpoint.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nb_exclusions.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c parallel.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c sgld.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c bintraj.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nebread.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c neb.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c runfiles.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c amd.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c gamd.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c scaledMD.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nfe_lib.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nfe_colvar.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nfe_pmd.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nfe_abmd.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nfe_stsm.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nfe_smd.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nfe_bbmd.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nfe_setup.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c get_cmdline.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c multipmemd.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c gb_force.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c gti.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c ene_frc_splines.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c offload_allocation.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nb_pairlist.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c nbips.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c angles_midpoint.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c dihedrals_midpoint.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c parallel_processor.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c loadbal.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pme_blk_recip.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pme_slab_recip.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pme_direct.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pme_fft_midpoint.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pme_recip_midpoint.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c dbg_arrays.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pme_force.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c emil.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c barostats.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c degcnt.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c relaxmd.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c constantph.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c constante.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c mcres.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c remd_exchg.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c runmd.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c runmin.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c veclib.F90 gcc -O3 -mtune=native -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pmemd_clib.c gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c gb_alltasks_setup.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pme_alltasks_setup.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native \ -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pme_setup.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c master_setup.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c pmemd.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c erfcfun.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c charmm_gold.F90 gfortran -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS -O3 -mtune=native -I/mnt/c/Users/Alen/Documents/Research/amber18//include -c get_efield_energy.F90 make -C ../../../AmberTools/src/emil install make[4]: Entering directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/emil' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/emil' gfortran -O3 -mtune=native -o /mnt/c/Users/Alen/Documents/Research/amber18//bin/pmemd gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o mdin_emil_dat.o mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o emil.o img.o nbips.o offload_allocation.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o nebread.o neb.o pme_force.o pbc.o nb_pairlist.o gb_ene_hybrid.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o phmd.o gb_force.o timers.o pmemd_lib.o runfiles.o file_io.o AmberNetcdf.o bintraj.o binrestart.o pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o charmm.o charmm_gold.o findmask.o remd.o multipmemd.o remd_exchg.o amd.o gamd.o ti.o gbsa.o barostats.o scaledMD.o constantph.o constante.o energy_records.o constantph_dat.o constante_dat.o relaxmd.o sgld.o emap.o get_efield_energy.o gti.o processor.o parallel_processor.o pme_fft_midpoint.o pme_recip_midpoint.o dihedrals_midpoint.o angles_midpoint.o bonds_midpoint.o dbg_arrays.o mcres.o ensure_alloc.o -L/mnt/c/Users/Alen/Documents/Research/amber18//lib \ /mnt/c/Users/Alen/Documents/Research/amber18//lib/libnetcdff.a /mnt/c/Users/Alen/Documents/Research/amber18//lib/libnetcdf.a -larpack -llapack -lblas -lxblas-amb /mnt/c/Users/Alen/Documents/Research/amber18//lib/libemil.a -lstdc++ nfe_lib.o nfe_setup.o nfe_colvar.o nfe_smd.o nfe_abmd.o nfe_pmd.o nfe_bbmd.o nfe_stsm.o make[3]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/src/pmemd/src' Installation of pmemd complete make[2]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/src/pmemd' Installation of Amber18 (serial) is complete at Tue Nov 5 16:45:22 EST 2019. make[1]: Leaving directory '/mnt/c/Users/Alen/Documents/Research/amber18/src'