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

sh: line 1: 48490 Abort trap: 6           /Users/JEAdams/amber16/bin/teLeap -s -f leap.in -I/Users/JEAdams/amber16/dat/leap/cmd -I/Users/JEAdams/amber16/dat/leap/parm -I/Users/JEAdams/amber16/dat/leap/prep -I/Users/JEAdams/amber16/dat/leap/lib > tleap.out
./Run.prm: Program error
make[3]: *** [prm_test] Error 1
Running test to create a simple mmCIF file 

Formal charge is 0
Name is (2R)-3,3-dimethylbutan-2-amine
diffing gbrna.cif.check with gbrna.cif
PASSED
==============================================================
==============================================================
cd sustiva && ./Run.sustiva
/Users/JEAdams/amber16/bin/tleap: line 10: 75572 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
diffing sustiva.mol2.save with sustiva.mol2
PASSED
==============================================================
===================================
cd mdgx/1p7e && ./Test.1p7e
/Users/JEAdams/amber16/bin/tleap: line 10: 76382 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
GetPrmTop >> Error.  Topology file prmtop contains no data.
grep: gb30.out: No such file or directory
grep: gb30.out: No such file or directory
grep: gb30.out: No such file or directory
diffing energy.dat.save with energy.dat
possible FAILURE:  check energy.dat.dif
==============================================================

cd mdgx/ForceCalc && ./Test.frcc
/Users/JEAdams/amber16/bin/tleap: line 10: 76586 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
GetPrmTop >> Error.  Topology file prmtop contains no data.
grep: forcedump.m: No such file or directory
grep: forcedump.m: No such file or directory
grep: forcedump.m: No such file or directory
grep: forcedump.m: No such file or directory
grep: forcedump.m: No such file or directory
grep: forcedump.m: No such file or directory
diffing frceval.dat.save with frceval.dat
file ddtmp.frceval.dat is short
possible FAILURE:  check frceval.dat.dif
==============================================================
==============================================================
cd leap && /Applications/Xcode.app/Contents/Developer/usr/bin/make -k test
/Applications/Xcode.app/Contents/Developer/usr/bin/make test.complete test.leap
AmberTools 16

Test OL3 Chi parameters for RNA.

/Users/JEAdams/amber16/bin/tleap: line 10: 76979 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
Program error
make[4]: [test.ol3] Error 1 (ignored)
AmberTools 16

Test Yildirim et al Chi parameters for RNA.

/Users/JEAdams/amber16/bin/tleap: line 10: 76988 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
Program error
make[4]: [test.yil] Error 1 (ignored)
AmberTools 16

Test Yildirim et al Chi parameters for RNA r(GACU).

/Users/JEAdams/amber16/bin/tleap: line 10: 76999 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
Program error
make[4]: [test.yil] Error 1 (ignored)

Test parameters for protein/DNA/RNA system.

AmberTools 16
/Users/JEAdams/amber16/bin/tleap: line 10: 77009 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
Program error
make[4]: [test.ff14sb.ol3.bsc0] Error 1 (ignored)

Test BSC0 parameters.

AmberTools 16
/Users/JEAdams/amber16/bin/tleap: line 10: 77018 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
Program error
make[4]: [test.bsc0] Error 1 (ignored)

Test BSC1 parameters.

AmberTools 16
/Users/JEAdams/amber16/bin/tleap: line 10: 77027 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
Program error
make[4]: [test.bsc1] Error 1 (ignored)

Test OL15 parameters.

AmberTools 16
/Users/JEAdams/amber16/bin/tleap: line 10: 77036 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
Program error
make[4]: [test.ol15] Error 1 (ignored)
AmberTools 16

Test GB radii assignments.

Radii set: bondi
/Users/JEAdams/amber16/bin/tleap: line 10: 77045 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
Program error
make[4]: [test.pbradii] Error 1 (ignored)
AMBERHOME is set to /Users/JEAdams/amber16
    building force field libraries:

        '94 ff..

diffing /Users/JEAdams/amber16/dat/leap/lib/all_amino94.lib with all_amino94.lib
PASSED
==============================================================

    loadpdb and saveamberparm: 94 ff..

./Run.tleap:  Program error in leap
make[4]: [test.leap] Error 1 (ignored)

         Creating a new-style (Amber 7) topology file 

/Users/JEAdams/amber16/bin/tleap: line 10: 77199 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
diffing trx.parm7.save with trx.parm7
possible FAILURE:  check trx.parm7.dif
==============================================================
possible FAILURE:  file trx.solv.parm7 does not exist.
==============================================================
/Users/JEAdams/amber16/bin/tleap: line 10: 77233 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
diffing gaff_wildcrd.parm7.save with gaff_wildcrd.parm7
possible FAILURE:  check gaff_wildcrd.parm7.dif
==============================================================

         Test of several LEaP features

/Users/JEAdams/amber16/bin/tleap: line 10: 77268 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
diffing sys1.mbondi2.parm7.save with sys1.mbondi2.parm7
possible FAILURE:  check sys1.mbondi2.parm7.dif
==============================================================
possible FAILURE:  file sys2.mbondi2.parm7 does not exist.
==============================================================
possible FAILURE:  file sys1.mbondi2.rst7 does not exist.
==============================================================
possible FAILURE:  file sys1_sys2.mbondi.parm7 does not exist.
==============================================================
possible FAILURE:  file sys1_sys2.mbondi.rst7 does not exist.
==============================================================
possible FAILURE:  file d_glu.bondi.parm7 does not exist.
==============================================================
possible FAILURE:  file d_glu.bondi.rst7 does not exist.
==============================================================
diffing alphabet.pdb.save with alphabet.pdb
PASSED
==============================================================
diffing alphabet2.pdb.save with alphabet2.pdb
PASSED
==============================================================
possible FAILURE:  file alphabet_wet.pdb does not exist.
==============================================================
possible FAILURE:  file alphabet2_wet.pdb does not exist.
==============================================================

         Creating a new-style (Amber 7) topology file with mbondi3 

/Users/JEAdams/amber16/bin/tleap: line 10: 77363 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
diffing alphabet.mbondi3.parm7.save with alphabet.mbondi3.parm7
possible FAILURE:  check alphabet.mbondi3.parm7.dif
==============================================================

         Checking that addIons neutralizes as well as possible

/Users/JEAdams/amber16/bin/tleap: line 10: 77398 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
possible FAILURE:  file neg_lys_addions.parm7 does not exist.
==============================================================
**
Testing prmtop and inpcrd built by tleap with GLYCAM_06j.
**
diffing Branches.parm7.save with Branches.parm7
file ddtmp.Branches.parm7 is short
possible FAILURE:  check Branches.parm7.dif
==============================================================
During the test of files Branches.rst7.save and Branches.rst7, there was an
Error:  Test output file Branches.rst7 not found.
==============================================================
diffing Chains.parm7.save with Chains.parm7
file ddtmp.Chains.parm7 is short
possible FAILURE:  check Chains.parm7.dif
==============================================================
During the test of files Chains.rst7.save and Chains.rst7, there was an
Error:  Test output file Chains.rst7 not found.
==============================================================
diffing Derivatives.parm7.save with Derivatives.parm7
file ddtmp.Derivatives.parm7 is short
possible FAILURE:  check Derivatives.parm7.dif
==============================================================
During the test of files Derivatives.rst7.save and Derivatives.rst7, there was an
Error:  Test output file Derivatives.rst7 not found.
==============================================================
diffing Solvate_Ion.parm7.save with Solvate_Ion.parm7
file ddtmp.Solvate_Ion.parm7 is short
possible FAILURE:  check Solvate_Ion.parm7.dif
==============================================================
During the test of files Solvate_Ion.rst7.save and Solvate_Ion.rst7, there was an
Error:  Test output file Solvate_Ion.rst7 not found.
==============================================================

**
Testing prmtop and inpcrd built by tleap with GLYCAM_06EPb.
**
diffing EP.parm7.save with EP.parm7
PASSED
==============================================================
diffing EP.rst7.save with EP.rst7
PASSED
==============================================================
diffing Solvate.parm7.save with Solvate.parm7
PASSED
==============================================================
diffing Solvate.rst7.save with Solvate.rst7
PASSED
==============================================================

**
Testing prmtop and inpcrd built by tleap with GLYCAM_06j_10.
**
diffing Glycoprotein.parm7.save with Glycoprotein.parm7
file ddtmp.Glycoprotein.parm7 is short
possible FAILURE:  check Glycoprotein.parm7.dif
==============================================================
During the test of files Glycoprotein.rst7.save and Glycoprotein.rst7, there was an
Error:  Test output file Glycoprotein.rst7 not found.
==============================================================

**
Testing prmtop and inpcrd built by tleap with GLYCAM_06j_12SB.
**
diffing Glycoprotein.parm7.save with Glycoprotein.parm7
file ddtmp.Glycoprotein.parm7 is short
possible FAILURE:  check Glycoprotein.parm7.dif
==============================================================
During the test of files Glycoprotein.rst7.save and Glycoprotein.rst7, there was an
Error:  Test output file Glycoprotein.rst7 not found.
==============================================================
==============================================================
==============================================================
# TODO: not work with --prefix yet since
# pymsmt uses lib in its source folder (AmberTools/src/pymsmt/lib)
cd pymsmt/mcpb/g03 && ./Run.pymsmt
/Users/JEAdams/amber16/bin/tleap: line 10: 87450 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
diffing 1A5T_small.pdb.save with 1A5T_small.pdb
PASSED
==============================================================
==============================================================
cd pymsmt/mcpb/g09 && ./Run.pymsmt
/Users/JEAdams/amber16/bin/tleap: line 10: 88129 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
diffing 1A5T_small.pdb.save with 1A5T_small.pdb
PASSED
==============================================================
==============================================================
diffing 1A5T_dry.prmtop.save with 1A5T_dry.prmtop
possible FAILURE:  check 1A5T_dry.prmtop.dif
==============================================================
possible FAILURE:  file 1A5T_dry.inpcrd does not exist.
==============================================================
diffing 1A5T_dry.pdb.save with 1A5T_dry.pdb
PASSED
==============================================================
possible FAILURE:  file 1A5T_solv.prmtop does not exist.
==============================================================
possible FAILURE:  file 1A5T_solv.inpcrd does not exist.
==============================================================
possible FAILURE:  file 1A5T_solv.pdb does not exist.
==============================================================
cd pymsmt/mcpb/gms && ./Run.pymsmt
/Users/JEAdams/amber16/bin/tleap: line 10: 88808 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
diffing 1A5T_small.pdb.save with 1A5T_small.pdb
PASSED

diffing 1A5T_tleap.in.save with 1A5T_tleap.in
PASSED
==============================================================
diffing 1A5T_dry.prmtop.save with 1A5T_dry.prmtop
possible FAILURE:  check 1A5T_dry.prmtop.dif
==============================================================
possible FAILURE:  file 1A5T_dry.inpcrd does not exist.
==============================================================
diffing 1A5T_dry.pdb.save with 1A5T_dry.pdb
PASSED
==============================================================
possible FAILURE:  file 1A5T_solv.prmtop does not exist.
==============================================================
possible FAILURE:  file 1A5T_solv.inpcrd does not exist.
==============================================================
possible FAILURE:  file 1A5T_solv.pdb does not exist.
==============================================================