cd src && make -f Makefile_at install make[1]: Entering directory `/usr/local/amber12/AmberTools/src/cpptraj/src' g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o main.o main.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o AmberParm.o AmberParm.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Frame.o Frame.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o CpptrajState.o CpptrajState.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ArgList.o ArgList.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o PtrajMask.o PtrajMask.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Distance.o Action_Distance.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ParmFileList.o ParmFileList.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o TrajinList.o TrajinList.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o TrajoutList.o TrajoutList.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ReferenceList.o ReferenceList.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o CoordFileList.o CoordFileList.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ActionList.o ActionList.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o DataSet.o DataSet.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o DataSetList.o DataSetList.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o vectormath.o vectormath.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o FrameList.o FrameList.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Rmsd.o Action_Rmsd.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Dihedral.o Action_Dihedral.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o DataFile.o DataFile.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o DataFileList.o DataFileList.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o CpptrajFile.o CpptrajFile.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o PDBfileRoutines.o PDBfileRoutines.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_AtomMap.o Action_AtomMap.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o FileIO.o FileIO.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o FileIO_Std.o FileIO_Std.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o FileIO_Gzip.o FileIO_Gzip.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Angle.o Action_Angle.cpp gcc -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o MpiRoutines.o MpiRoutines.c g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o FileIO_Mpi.o FileIO_Mpi.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Strip.o Action_Strip.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action.o Action.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o AtomMask.o AtomMask.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o DataSet_double.o DataSet_double.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_DSSP.o Action_DSSP.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o DataSet_string.o DataSet_string.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Center.o Action_Center.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o FileIO_Bzip2.o FileIO_Bzip2.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Hbond.o Action_Hbond.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o DataSet_integer.o DataSet_integer.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Image.o Action_Image.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Surf.o Action_Surf.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Radgyr.o Action_Radgyr.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Mask.o Action_Mask.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Closest.o Action_Closest.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o NetcdfRoutines.o NetcdfRoutines.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o CpptrajStdio.o CpptrajStdio.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_AutoImage.o Action_AutoImage.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Mol2FileRoutines.o Mol2FileRoutines.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_NAstruct.o Action_NAstruct.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o DistRoutines.o DistRoutines.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o AxisType.o AxisType.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o TorsionRoutines.o TorsionRoutines.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Pucker.o Action_Pucker.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Range.o Range.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Outtraj.o Action_Outtraj.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Rms2d.o Action_Rms2d.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ProgressBar.o ProgressBar.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o TrajectoryIO.o TrajectoryIO.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o TrajectoryFile.o TrajectoryFile.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o BoxType.o BoxType.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o CharBuffer.o CharBuffer.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Traj_AmberCoord.o Traj_AmberCoord.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Traj_AmberNetcdf.o Traj_AmberNetcdf.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Traj_PDBfile.o Traj_PDBfile.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Traj_AmberRestart.o Traj_AmberRestart.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Traj_Mol2File.o Traj_Mol2File.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Traj_AmberRestartNC.o Traj_AmberRestartNC.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Traj_Conflib.o Traj_Conflib.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o RemdTraj.o RemdTraj.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Name.o Name.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Average.o Action_Average.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Histogram.o Histogram.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Analysis.o Analysis.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_DistRmsd.o Action_DistRmsd.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o AnalysisList.o AnalysisList.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Analysis_Hist.o Analysis_Hist.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o DataSet_XYZ.o DataSet_XYZ.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Radial.o Action_Radial.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Jcoupling.o Action_Jcoupling.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o TriangleMatrix.o TriangleMatrix.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Clustering.o Action_Clustering.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ClusterList.o ClusterList.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Traj_CharmmDcd.o Traj_CharmmDcd.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Bonds.o Bonds.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o FileRoutines.o FileRoutines.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Pairwise.o Action_Pairwise.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o DataSet_float.o DataSet_float.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o CoordList.o CoordList.cpp gcc -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ptraj_stack.o ptraj_stack.c gcc -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ptraj_actions.o ptraj_actions.c g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_PtrajAction.o Action_PtrajAction.cpp gcc -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ptraj_analyze.o ptraj_analyze.c gcc -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ptraj_evec.o ptraj_evec.c gcc -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ptraj_common.o ptraj_common.c gcc -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ptraj_arg.o ptraj_arg.c gcc -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ptraj_state.o ptraj_state.c gcc -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ptraj_scalar.o ptraj_scalar.c g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Analysis_PtrajAnalysis.o Analysis_PtrajAnalysis.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ptraj_convert.o ptraj_convert.cpp gcc -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o molsurf.o molsurf.c g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Molsurf.o Action_Molsurf.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_CheckStructure.o Action_CheckStructure.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_DihedralScan.o Action_DihedralScan.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_Rotdif.o Action_Rotdif.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Random.o Random.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Integrate.o Integrate.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Analysis_Corr.o Analysis_Corr.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_RunningAvg.o Action_RunningAvg.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Action_RmsAvgCorr.o Action_RmsAvgCorr.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o DataSet_Matrix.o DataSet_Matrix.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ParmFile.o ParmFile.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Parm_Amber.o Parm_Amber.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Parm_PDB.o Parm_PDB.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Parm_Mol2.o Parm_Mol2.cpp g++ -c -I/usr/local/amber12/include -O3 -mtune=native -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o Parm_CharmmPsf.o Parm_CharmmPsf.cpp gfortran -c -ffree-form -O3 -mtune=native -I/usr/local/amber12/include -o thermo.o ../../ptraj/thermo.F90 gfortran -c -ffree-form -O3 -mtune=native -I/usr/local/amber12/include -o pubfft.o ../../ptraj/pubfft.F90 g++ -static -o cpptraj main.o AmberParm.o Frame.o CpptrajState.o ArgList.o PtrajMask.o Action_Distance.o ParmFileList.o TrajinList.o TrajoutList.o ReferenceList.o CoordFileList.o ActionList.o DataSet.o DataSetList.o vectormath.o FrameList.o Action_Rmsd.o Action_Dihedral.o DataFile.o DataFileList.o CpptrajFile.o PDBfileRoutines.o Action_AtomMap.o FileIO.o FileIO_Std.o FileIO_Gzip.o Action_Angle.o MpiRoutines.o FileIO_Mpi.o Action_Strip.o Action.o AtomMask.o DataSet_double.o Action_DSSP.o DataSet_string.o Action_Center.o FileIO_Bzip2.o Action_Hbond.o DataSet_integer.o Action_Image.o Action_Surf.o Action_Radgyr.o Action_Mask.o Action_Closest.o NetcdfRoutines.o CpptrajStdio.o Action_AutoImage.o Mol2FileRoutines.o Action_NAstruct.o DistRoutines.o AxisType.o TorsionRoutines.o Action_Pucker.o Range.o Action_Outtraj.o Action_Rms2d.o ProgressBar.o TrajectoryIO.o TrajectoryFile.o BoxType.o CharBuffer.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_PDBfile.o Traj_AmberRestart.o Traj_Mol2File.o Traj_AmberRestartNC.o Traj_Conflib.o RemdTraj.o Name.o Action_Average.o Histogram.o Analysis.o Action_DistRmsd.o AnalysisList.o Analysis_Hist.o DataSet_XYZ.o Action_Radial.o Action_Jcoupling.o TriangleMatrix.o Action_Clustering.o ClusterList.o Traj_CharmmDcd.o Bonds.o FileRoutines.o Action_Pairwise.o DataSet_float.o CoordList.o ptraj_stack.o ptraj_actions.o Action_PtrajAction.o ptraj_analyze.o ptraj_evec.o ptraj_common.o ptraj_arg.o ptraj_state.o ptraj_scalar.o Analysis_PtrajAnalysis.o ptraj_convert.o molsurf.o Action_Molsurf.o Action_CheckStructure.o Action_DihedralScan.o Action_Rotdif.o Random.o Integrate.o Analysis_Corr.o Action_RunningAvg.o Action_RmsAvgCorr.o DataSet_Matrix.o ParmFile.o Parm_Amber.o Parm_PDB.o Parm_Mol2.o Parm_CharmmPsf.o thermo.o pubfft.o \ -L/usr/local/amber12/lib -lz -lbz2 -larpack -llapack -lblas -static -lgfortran -w /usr/bin/ld: cannot find -lbz2 collect2: ld returned 1 exit status make[1]: *** [cpptraj] Error 1 make[1]: Leaving directory `/usr/local/amber12/AmberTools/src/cpptraj/src' make: *** [install] Error 2