mjhsieh@ubuntu:~/amber11/AmberTools/test$ uname -a Linux ubuntu 2.6.32-22-generic #33-Ubuntu SMP Wed Apr 28 13:28:05 UTC 2010 x86_64 GNU/Linux mjhsieh@ubuntu:~/amber11/AmberTools/test$ export AMBERHOME=/home/mjhsieh/amber11 mjhsieh@ubuntu:~/amber11/AmberTools/test$ make test.leap cd leap && ./Run.tleap AMBERHOME is set to /home/mjhsieh/amber11 Running leap tests on ./tleap -> ../../exe/teLeap building force field libraries: '91 ff.. diffing /home/mjhsieh/amber11/dat/leap/lib/all_amino91.lib with all_amino91.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/all_aminoct91.lib with all_aminoct91.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/all_aminont91.lib with all_aminont91.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/all_nucleic91.lib with all_nucleic91.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/ions91.lib with ions91.lib PASSED ============================================================== '94 ff.. diffing /home/mjhsieh/amber11/dat/leap/lib/all_amino94.lib with all_amino94.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/all_aminoct94.lib with all_aminoct94.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/all_aminont94.lib with all_aminont94.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/all_nucleic94.lib with all_nucleic94.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/ions94.lib with ions94.lib PASSED ============================================================== loadpdb and saveamberparm: 94 ff.. ./Run.tleap: Program error in leap make: *** [test.leap] Error 1 mjhsieh@ubuntu:~/amber11/AmberTools/test$ pushd ../../.. ~/ ~/amber11/AmberTools/test mjhsieh@ubuntu:~$ amber11/bin/tleap -f leaprc.GLYCAM_06 -I: Adding /home/mjhsieh/amber11/dat/leap/prep to search path. -I: Adding /home/mjhsieh/amber11/dat/leap/lib to search path. -I: Adding /home/mjhsieh/amber11/dat/leap/parm to search path. -I: Adding /home/mjhsieh/amber11/dat/leap/cmd to search path. -f: Source leaprc.GLYCAM_06. Welcome to LEaP! (no leaprc in search path) Sourcing: /home/mjhsieh/amber11/dat/leap/cmd/leaprc.GLYCAM_06 Loading parameters: /home/mjhsieh/amber11/dat/leap/parm/Glycam_06g.dat Reading title: GLYCAM PARAMETERS (FOR AMBER 8.0, RESP 0.010), COPYRIGHT CCRC 2004 Loading Prep file: /home/mjhsieh/amber11/dat/leap/prep/GLYCAM_06.prep Loading library: /home/mjhsieh/amber11/dat/leap/lib/GLYCAM_amino_06.lib Segmentation fault mjhsieh@ubuntu:~$ cd amber11 mjhsieh@ubuntu:~/amber11$ patch -p0 < ~/leap.patch patching file AmberTools/src/leap/src/leap/database.c patching file AmberTools/src/leap/src/leap/sort.c patching file AmberTools/src/leap/src/leap/stringExtra.c mjhsieh@ubuntu:~/amber11$ cd AmberTools/src/leap/ mjhsieh@ubuntu:~/amber11/AmberTools/src/leap$ make install Compiling basic programs cd src/leap && make installteLeap make[1]: Entering directory `/home/mjhsieh/amber11/AmberTools/src/leap/src/leap' gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o stringExtra.o stringExtra.c gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o sort.o sort.c gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o database.o database.c gcc -o utilMakeHelp basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o utilMakeHelp.o -lm ./utilMakeHelp helptext.text helptext.c gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o helptext.o helptext.c gcc -o teLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o collection.o container.o internal.o list.o loop.o molecule.o oDouble.o oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o graphUtil.o select.o amber.o build.o elements.o library.o chirality.o minimizer.o model.o parmLib.o pdbFile.o mol2File.o tools.o variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o restraint.o hybrid.o tLeap.o -lm mv teLeap /home/mjhsieh/amber11/bin make[1]: Leaving directory `/home/mjhsieh/amber11/AmberTools/src/leap/src/leap' Copying shell script cp tleap /home/mjhsieh/amber11/bin/tleap chmod +x /home/mjhsieh/amber11/bin/tleap make install_xleap make[1]: Entering directory `/home/mjhsieh/amber11/AmberTools/src/leap' cd src/Wc && make make[2]: Entering directory `/home/mjhsieh/amber11/AmberTools/src/leap/src/Wc' make[2]: `libWcLeap.a' is up to date. make[2]: Leaving directory `/home/mjhsieh/amber11/AmberTools/src/leap/src/Wc' cd src/Xmu && make make[2]: Entering directory `/home/mjhsieh/amber11/AmberTools/src/leap/src/Xmu' make[2]: `libXmu.a' is up to date. make[2]: Leaving directory `/home/mjhsieh/amber11/AmberTools/src/leap/src/Xmu' cd src/Xpm && make make[2]: Entering directory `/home/mjhsieh/amber11/AmberTools/src/leap/src/Xpm' make[2]: `libXpm.a' is up to date. make[2]: Leaving directory `/home/mjhsieh/amber11/AmberTools/src/leap/src/Xpm' cd src/Xraw && make make[2]: Entering directory `/home/mjhsieh/amber11/AmberTools/src/leap/src/Xraw' make[2]: `libXaw.a' is up to date. make[2]: Leaving directory `/home/mjhsieh/amber11/AmberTools/src/leap/src/Xraw' cd src/leap && make install make[2]: Entering directory `/home/mjhsieh/amber11/AmberTools/src/leap/src/leap' gcc -o teLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o collection.o container.o internal.o list.o loop.o molecule.o oDouble.o oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o graphUtil.o select.o amber.o build.o elements.o library.o chirality.o minimizer.o model.o parmLib.o pdbFile.o mol2File.o tools.o variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o restraint.o hybrid.o tLeap.o -lm gcc -o xaLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o collection.o container.o internal.o list.o loop.o molecule.o oDouble.o oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o graphUtil.o select.o amber.o build.o elements.o library.o chirality.o minimizer.o model.o parmLib.o pdbFile.o mol2File.o tools.o variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o restraint.o hybrid.o xTank.o xAction.o x3d.o xBasics.o xaLeapc.o xaUnitEditor.o xaTable.o xaAtomTable.o XrawRegistr.o xaCommand.o xaTools.o xaAtomParmTable.o xaBondParmTable.o xaAngleParmTable.o xaParmEditor.o xaTorsionParmTable.o xaImproperParmTable.o xaHBondParmTable.o ../Xraw/libXaw.a ../Wc/libWcLeap.a ../Xpm/libXpm.a ../Xmu/libXmu.a -L/usr/lib64 -L/usr/lib -lXt -lXext -lSM -lICE -lX11 -lXau -lXdmcp -lm -lpthread ../Xraw/libXaw.a(AsciiSrc.o): In function `InitStringOrFile': AsciiSrc.c:(.text+0x136a): warning: the use of `tmpnam' is dangerous, better use `mkstemp' m4 xaLeap.rm4 > XaLeap_wcl mv teLeap xaLeap /home/mjhsieh/amber11/bin mv XaLeap_wcl /home/mjhsieh/amber11/dat make[2]: Leaving directory `/home/mjhsieh/amber11/AmberTools/src/leap/src/leap' Copying shell script cp xleap /home/mjhsieh/amber11/bin/xleap chmod +x /home/mjhsieh/amber11/bin/xleap Copying pixmaps mkdir /home/mjhsieh/amber11/dat/pixmap mkdir: cannot create directory `/home/mjhsieh/amber11/dat/pixmap': File exists make[1]: [install_xleap] Error 1 (ignored) cd pixmap; /bin/cp * /home/mjhsieh/amber11/dat/pixmap Finished with the install of LEaP make[1]: Leaving directory `/home/mjhsieh/amber11/AmberTools/src/leap' mjhsieh@ubuntu:~/amber11/AmberTools/src/leap$ mjhsieh@ubuntu:~/amber11/AmberTools/test$ make test.leap cd leap && ./Run.tleap AMBERHOME is set to /home/mjhsieh/amber11 Running leap tests on ./tleap -> ../../exe/teLeap building force field libraries: '91 ff.. diffing /home/mjhsieh/amber11/dat/leap/lib/all_amino91.lib with all_amino91.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/all_aminoct91.lib with all_aminoct91.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/all_aminont91.lib with all_aminont91.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/all_nucleic91.lib with all_nucleic91.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/ions91.lib with ions91.lib PASSED ============================================================== '94 ff.. diffing /home/mjhsieh/amber11/dat/leap/lib/all_amino94.lib with all_amino94.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/all_aminoct94.lib with all_aminoct94.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/all_aminont94.lib with all_aminont94.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/all_nucleic94.lib with all_nucleic94.lib PASSED ============================================================== diffing /home/mjhsieh/amber11/dat/leap/lib/ions94.lib with ions94.lib PASSED ============================================================== loadpdb and saveamberparm: 94 ff.. - aminoan94 comparing topology to earlier leap version.. diffing ff94/all_aminoan94.top with all_aminoan94.top PASSED ============================================================== - aminonc94 comparing topology to earlier leap version.. diffing ff94/all_aminonc94.top with all_aminonc94.top PASSED ============================================================== - dna94 comparing topology to earlier leap version.. diffing ff94/all_dna94.top with all_dna94.top PASSED ============================================================== - rna94 comparing topology to earlier leap version.. diffing ff94/all_rna94.top with all_rna94.top PASSED ============================================================== -------------------------------------------------------------- Notes: - If all tests PASSED, you can 'rm *.log *.out *.lib *.top' - For a discussion of energy differences (sander*.dif) see 0README. - It is common to see round-off differences in the portion of these tests -------------------------------------------------------------- mjhsieh@ubuntu:~/amber11/AmberTools/test$ cd mjhsieh@ubuntu:~$ amber11/bin/tleap -f leaprc.GLYCAM_06 -I: Adding /home/mjhsieh/amber11/dat/leap/prep to search path. -I: Adding /home/mjhsieh/amber11/dat/leap/lib to search path. -I: Adding /home/mjhsieh/amber11/dat/leap/parm to search path. -I: Adding /home/mjhsieh/amber11/dat/leap/cmd to search path. -f: Source leaprc.GLYCAM_06. Welcome to LEaP! (no leaprc in search path) Sourcing: /home/mjhsieh/amber11/dat/leap/cmd/leaprc.GLYCAM_06 Loading parameters: /home/mjhsieh/amber11/dat/leap/parm/Glycam_06g.dat Reading title: GLYCAM PARAMETERS (FOR AMBER 8.0, RESP 0.010), COPYRIGHT CCRC 2004 Loading Prep file: /home/mjhsieh/amber11/dat/leap/prep/GLYCAM_06.prep Loading library: /home/mjhsieh/amber11/dat/leap/lib/GLYCAM_amino_06.lib Loading library: /home/mjhsieh/amber11/dat/leap/lib/GLYCAM_aminoct_06.lib Loading library: /home/mjhsieh/amber11/dat/leap/lib/GLYCAM_aminont_06.lib Loading library: /home/mjhsieh/amber11/dat/leap/lib/solvents.lib > x=sequence{ROH 0GB} > desc x UNIT name: ROH Head atom: .R.A Tail atom: .R<0GB 2>.A Contents: R R<0GB 2> > set x head x.2.O2 > desc x UNIT name: ROH Head atom: .R<0GB 2>.A Tail atom: .R<0GB 2>.A Contents: R R<0GB 2> > quit Quit