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configure.smog2
docker/Dockerfile.SMOG-OpenSMOG.s2.4.4-os1.1
docker/README.docker
docker/docker.create.bash
docker/docker.create.educational.bash
docker/Dockerfile.gitversion
docker/Dockerfile.v2.4.5
docker/Dockerfile.v2.4.4
SMOG-CHECK/scm-check
SMOG-CHECK/smog-tool-check
SMOG-CHECK/checkall
SMOG-CHECK/README.smogcheck
SMOG-CHECK/smog-check
SMOG-CHECK/share/residues/ligands
SMOG-CHECK/share/residues/list.CA
SMOG-CHECK/share/residues/list.AA
SMOG-CHECK/share/residues/nucleicacids
SMOG-CHECK/share/residues/list.CAgauss
SMOG-CHECK/share/residues/ions
SMOG-CHECK/share/residues/list.AAgauss
SMOG-CHECK/share/residues/glycans
SMOG-CHECK/share/residues/bonds_by_residue.AA
SMOG-CHECK/share/residues/aminoacids
SMOG-CHECK/share/backboneatoms/ligands
SMOG-CHECK/share/backboneatoms/nucleicacids
SMOG-CHECK/share/backboneatoms/glycans
SMOG-CHECK/share/backboneatoms/aminoacids
SMOG-CHECK/share/PDB.files/mangled.resnames.pdb
SMOG-CHECK/share/PDB.files/3PTA.pdb
SMOG-CHECK/share/PDB.files/2FP4-GTP.pdb
SMOG-CHECK/share/PDB.files/4gvy.pdb
SMOG-CHECK/share/PDB.files/DNA.terminal.BMG.pdb
SMOG-CHECK/share/PDB.files/glycans.BOND.pdb
SMOG-CHECK/share/PDB.files/DNA.terminal.pdb
SMOG-CHECK/share/PDB.files/1AKEapo_v2.pdb
SMOG-CHECK/share/PDB.files/6qnr-partIns.pdb
SMOG-CHECK/share/PDB.files/protein-RNA.pdb
SMOG-CHECK/share/PDB.files/1reschains_v2.pdb
SMOG-CHECK/share/PDB.files/1A01-ADP+RNA.pdb
SMOG-CHECK/share/PDB.files/2ci2_v2.pdb
SMOG-CHECK/share/PDB.files/1A01-AMP.pdb
SMOG-CHECK/share/PDB.files/large.gro
SMOG-CHECK/share/PDB.files/tRNA.pdb
SMOG-CHECK/share/PDB.files/1A01-ATP.pdb
SMOG-CHECK/share/PDB.files/tRNA.chop.pdb
SMOG-CHECK/share/PDB.files/2ci2_v2.CB.pdb
SMOG-CHECK/share/PDB.files/1AKEapo_v3.BOND.pdb
SMOG-CHECK/share/PDB.files/mangled.atomnames.pdb
SMOG-CHECK/share/PDB.files/3PTA.preadjust.pdb
SMOG-CHECK/share/PDB.files/2ci2_v2.contacts
SMOG-CHECK/share/PDB.files/2ci2_v2.freecoor.pdb
SMOG-CHECK/share/PDB.files/terminaltest.pdb
SMOG-CHECK/share/PDB.files/all.pdbs
SMOG-CHECK/share/PDB.files/2FP4-GDP.pdb
SMOG-CHECK/share/PDB.files/1AKEapo_v3.NOBOND.pdb
SMOG-CHECK/share/PDB.files/2FP4-GDP.largeformat.pdb
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SMOG-CHECK/share/PDB.files/1F4N_v2.pdb
SMOG-CHECK/share/PDB.files/terminaltest.BOND.pdb
SMOG-CHECK/share/PDB.files/mangled.resnames.altlocs.pdb
SMOG-CHECK/share/PDB.files/sample.AA.ndx
SMOG-CHECK/share/PDB.files/mangled.atomnames.lf.pdb
SMOG-CHECK/share/PDB.files/3IZH_v2.pdb
SMOG-CHECK/share/PDB.files/1A01-ADP.pdb
SMOG-CHECK/share/PDB.files/FES.pdb
SMOG-CHECK/share/PDB.files/in.groups
SMOG-CHECK/share/PDB.files/3IZH_v2.CB.pdb
SMOG-CHECK/share/PDB.files/full.pre.pdb
SMOG-CHECK/share/PDB.files/2ci2.official.pdb
SMOG-CHECK/share/PDB.files/large.ndx
SMOG-CHECK/share/PDB.files/1cis.nearofficial.pdb
SMOG-CHECK/share/mapfiles/sbmMapExact.alts
SMOG-CHECK/share/mapfiles/sbmMapExact.lf.alts
SMOG-CHECK/share/refs/extras.ref.dihedraltypes
SMOG-CHECK/share/refs/make.extras.ref.bash
SMOG-CHECK/share/refs/extras.ref.bondtypes
SMOG-CHECK/share/refs/extras.ref.angletypes
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SMOG-CHECK/share/templates/SBM_AA_STATIC/AA-whitford09.sif
SMOG-CHECK/share/templates/SBM_AA_STATIC/AA-whitford09.nb
SMOG-CHECK/share/templates/SBM_AA_STATIC/AA-whitford09.bif
SMOG-CHECK/share/templates/SBM_AA_BOND/.notes
SMOG-CHECK/share/templates/SBM_AA_BOND/bond.b
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SMOG-CHECK/share/templates/SBM_AA_BOND/bond.bif
SMOG-CHECK/share/templates/SBM_AA_BOND/bond.sif
SMOG-CHECK/share/templates/SBM_match/comparelist
SMOG-CHECK/share/templates/SBM_match/atomtypes
SMOG-CHECK/share/templates/SBM_match/CB.b
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SMOG-CHECK/share/templates/SBM_match/CB.sif
SMOG-CHECK/share/templates/SBM_2cg/AA-whitford09.b
SMOG-CHECK/share/templates/SBM_2cg/.citation
SMOG-CHECK/share/templates/SBM_2cg/AA-whitford09.sif
SMOG-CHECK/share/templates/SBM_2cg/AA-whitford09.nb
SMOG-CHECK/share/templates/SBM_2cg/AA-whitford09.bif
SMOG-CHECK/share/templates/SBM_calpha/CA-clementi00.bif
SMOG-CHECK/share/templates/SBM_calpha/CA-clementi00.nb
SMOG-CHECK/share/templates/SBM_calpha/.citation
SMOG-CHECK/share/templates/SBM_calpha/CA-clementi00.b
SMOG-CHECK/share/templates/SBM_calpha/CA-clementi00.sif
SMOG-CHECK/share/templates/SBM_cr2/AA-whitford09.b
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SMOG-CHECK/share/templates/SBM_AA/AA-whitford09.sif
SMOG-CHECK/share/templates/SBM_AA/AA-whitford09.gaussian.nb
SMOG-CHECK/share/templates/SBM_AA/extras.gmxtest
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SMOG-CHECK/share/templates/SBM_AA/AA-whitford09.bif
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SMOG-CHECK/share/templates/SBM_AA/extras
SMOG-CHECK/share/scm/templates/CI2/CI2.top
SMOG-CHECK/share/scm/templates/CI2/CI2.CA.contacts
SMOG-CHECK/share/scm/templates/CI2/CI2.gro
SMOG-CHECK/share/scm/templates/CI2/CI2.pdb
SMOG-CHECK/share/scm/templates/CI2/CI2.AA.contacts
SMOG-CHECK/share/scm/templates/CI2/CI2.AACA.contacts
SMOG-CHECK/src/scm-test.bash
SMOG-CHECK/src/cleanup.bash
SMOG-CHECK/src/check-tools.v2.pl
SMOG-CHECK/src/modules/check_adjust.pm
SMOG-CHECK/src/modules/check_ions.pm
SMOG-CHECK/src/modules/check_extract.pm
SMOG-CHECK/src/modules/check_scale.pm
SMOG-CHECK/src/modules/check_common.pm
SMOG-CHECK/src/modules/check_table.pm
SMOG-CHECK/src/check.v2.pl
README
COPYING
examples/gromacs2020/all-atom/2ci2.edr
examples/gromacs2020/all-atom/2ci2.top
examples/gromacs2020/all-atom/mdout.mdp
examples/gromacs2020/all-atom/2ci2.rename.pdb
examples/gromacs2020/all-atom/2ci2.cpt
examples/gromacs2020/all-atom/2ci2.trr
examples/gromacs2020/all-atom/2ci2.1chain.pdb
examples/gromacs2020/all-atom/terminaloutput
examples/gromacs2020/all-atom/2ci2.ndx
examples/gromacs2020/all-atom/allatom.smog.gromacs2020.mdp
examples/gromacs2020/all-atom/2ci2.contacts
examples/gromacs2020/all-atom/2ci2.xtc
examples/gromacs2020/all-atom/2ci2.log
examples/gromacs2020/all-atom/2ci2.tpr
examples/gromacs2020/all-atom/2ci2.gro
examples/gromacs2020/all-atom/2ci2.pdb
examples/gromacs2020/all-atom/2ci2.box.gro
examples/gromacs5/all-atom/centered.gro
examples/gromacs5/all-atom/traj_comp.xtc
examples/gromacs5/all-atom/smog.contacts
examples/gromacs5/all-atom/CI2.AA.pdb
examples/gromacs5/all-atom/smog.ndx
examples/gromacs5/all-atom/ener.edr
examples/gromacs5/all-atom/smog.top
examples/gromacs5/all-atom/confout.gro
examples/gromacs5/all-atom/allatomForGromacs5.mdp
examples/gromacs5/all-atom/terminalHistory
examples/gromacs5/all-atom/smog.gro
examples/gromacs5/all-atom/topol.tpr
examples/gromacs5/all-atom/md.log
examples/gromacs5/all-atom/state.cpt
examples/gromacs5/calpha/centered.gro
examples/gromacs5/calpha/traj_comp.xtc
examples/gromacs5/calpha/smog.contacts
examples/gromacs5/calpha/smog.ndx
examples/gromacs5/calpha/calphaForGromacs5.mdp
examples/gromacs5/calpha/ener.edr
examples/gromacs5/calpha/smog.top
examples/gromacs5/calpha/confout.gro
examples/gromacs5/calpha/terminalHistory
examples/gromacs5/calpha/smog.gro
examples/gromacs5/calpha/topol.tpr
examples/gromacs5/calpha/table1012.xvg
examples/gromacs5/calpha/md.log
examples/gromacs5/calpha/state.cpt
examples/whamExamples/1/dos
examples/whamExamples/1/coord
examples/whamExamples/1/config
examples/whamExamples/1/free/1450
examples/whamExamples/1/free/1460
examples/whamExamples/1/free/1380
examples/whamExamples/1/free/1540
examples/whamExamples/1/free/1500
examples/whamExamples/1/free/1360
examples/whamExamples/1/free/1530
examples/whamExamples/1/free/1350
examples/whamExamples/1/free/1480
examples/whamExamples/1/free/1420
examples/whamExamples/1/free/1410
examples/whamExamples/1/free/1400
examples/whamExamples/1/free/1490
examples/whamExamples/1/free/1430
examples/whamExamples/1/free/1520
examples/whamExamples/1/free/1510
examples/whamExamples/1/free/1370
examples/whamExamples/1/free/1390
examples/whamExamples/1/free/1470
examples/whamExamples/1/free/1440
examples/whamExamples/1/cv
examples/whamExamples/1/data/hist.144.2.in
examples/whamExamples/1/data/hist.144.3.in
examples/whamExamples/1/data/hist.144.4.in
examples/gromacs4/all-atom/traj.xtc
examples/gromacs4/all-atom/allatomForGromacs4.X.mdp
examples/gromacs4/all-atom/smog.contacts
examples/gromacs4/all-atom/CI2.AA.pdb
examples/gromacs4/all-atom/smog.ndx
examples/gromacs4/all-atom/ener.edr
examples/gromacs4/all-atom/smog.top
examples/gromacs4/all-atom/confout.gro
examples/gromacs4/all-atom/all-atom.tpr
examples/gromacs4/all-atom/terminalHistory
examples/gromacs4/all-atom/smog.gro
examples/gromacs4/all-atom/state_prev.cpt
examples/gromacs4/all-atom/md.log
examples/gromacs4/all-atom/state.cpt
examples/gromacs4/calpha/traj.xtc
examples/gromacs4/calpha/smog.contacts
examples/gromacs4/calpha/CI2.AA.pdb
examples/gromacs4/calpha/smog.ndx
examples/gromacs4/calpha/ener.edr
examples/gromacs4/calpha/smog.top
examples/gromacs4/calpha/confout.gro
examples/gromacs4/calpha/terminalHistory
examples/gromacs4/calpha/smog.gro
examples/gromacs4/calpha/calphaForGromacs4.X.mdp
examples/gromacs4/calpha/calpha.tpr
examples/gromacs4/calpha/table1012.xvg
examples/gromacs4/calpha/md.log
examples/gromacs4/calpha/state.cpt
examples/README
singularity/smog2.v2.4.4.def
singularity/osperl.def
singularity/build.singularity.remote.bash
singularity/smog2.v2.4.5-pre1.def
singularity/README.singularity
singularity/smog2.gitversion.def
THANKS
test-config
share/test/benchmark.pl
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share/test/benchmarks/1AKEapo_v2.AAgauss.pdb
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share/test/benchmarks/1AKEapo_v2.AA.top
share/test/benchmarks/makeBenchmarks.bash
share/test/benchmarks/2GIS_noSAM_v2.AA.pdb
share/test/benchmarks/1AKEapo_v2.AAgauss.top
share/test/benchmarks/1AKEapo_v2.CA.pdb
share/test/benchmarks/2GIS_noSAM_v2.AAgauss.pdb
share/java/argparser/BooleanHolder.java
share/java/argparser/ArgParser.java
share/java/argparser/IntHolder.class
share/java/argparser/ArgParser.class
share/java/argparser/ArgParserTest.class
share/java/argparser/StringScanner.java
share/java/argparser/DoubleHolder.java
share/java/argparser/ArgParserTest$MErr.class
share/java/argparser/CharHolder.class
share/java/argparser/BooleanHolder.class
share/java/argparser/ArgParser$NameDesc.class
share/java/argparser/StringScanner.class
share/java/argparser/SimpleExample.class
share/java/argparser/ArgParserTest$RngCheck.class
share/java/argparser/ArgParseException.class
share/java/argparser/ArgParser$Record.class
share/java/argparser/ArgParser$RangeAtom.class
share/java/argparser/FloatHolder.class
share/java/argparser/ArgParserTest.java
share/java/argparser/ArgParser$RangePnt.class
share/java/argparser/ObjectHolder.java
share/java/argparser/ObjectHolder.class
share/java/argparser/StringHolder.class
share/java/argparser/DoubleHolder.class
share/java/argparser/ArgParseException.java
share/java/argparser/SimpleExample.java
share/java/argparser/COPYRIGHT
share/java/argparser/ArgParserTest$MTest.class
share/java/argparser/StringHolder.java
share/java/argparser/FloatHolder.java
share/java/argparser/StringScanException.class
share/java/argparser/CharHolder.java
share/java/argparser/LongHolder.java
share/java/argparser/StringScanException.java
share/java/argparser/IntHolder.java
share/java/argparser/LongHolder.class
share/java/org/smogserver/util/Utilities.class
share/java/org/smogserver/util/ConnectionList.java
share/java/org/smogserver/util/SparseRealArray.java
share/java/org/smogserver/util/Utilities.java
share/java/org/smogserver/util/SparseIntegerArray.java
share/java/org/smogserver/util/math/Bin.java
share/java/org/smogserver/util/math/LinearAlgebra.java
share/java/org/smogserver/util/math/Stats.java
share/java/org/smogserver/util/math/NVector.java
share/java/org/smogserver/util/math/Bin.class
share/java/org/smogserver/util/math/LinearAlgebra.class
share/java/org/smogserver/util/math/NVector.class
share/java/org/smogserver/util/math/Complex.class
share/java/org/smogserver/util/math/Coordinates.java
share/java/org/smogserver/util/math/Algebra.java
share/java/org/smogserver/util/math/Algebra.class
share/java/org/smogserver/util/math/Stats.class
share/java/org/smogserver/util/math/SimpleDoubleBin.java
share/java/org/smogserver/util/math/Coordinates.class
share/java/org/smogserver/util/math/Complex.java
share/java/org/smogserver/util/math/SimpleDoubleBin.class
share/java/org/smogserver/util/NumberedList.java
share/java/org/smogserver/util/geom/JGrid3D.java
share/java/org/smogserver/util/geom/Geometry.class
share/java/org/smogserver/util/geom/Triangle.java
share/java/org/smogserver/util/geom/Sphere.class
share/java/org/smogserver/util/geom/JGridable3D.java
share/java/org/smogserver/util/geom/JGridable3D.class
share/java/org/smogserver/util/geom/Sphere.java
share/java/org/smogserver/util/geom/JGrid3D.class
share/java/org/smogserver/util/geom/Triangle.class
share/java/org/smogserver/util/geom/Geometry.java
share/java/org/smogserver/util/SparseDoubleArray.java
share/java/org/smogserver/util/exception/DoneException.class
share/java/org/smogserver/util/exception/DoneException.java
share/java/org/smogserver/util/ConnectionList.class
share/java/org/smogserver/io/FileIO.class
share/java/org/smogserver/io/FileIO.java
share/java/org/smogserver/io/CharValues.java
share/java/ral/Real.class
share/java/ral/Real$NumberFormat.class
share/java/ral/Real.java
share/schemas/sif.xsd
share/schemas/nb.xsd
share/schemas/b.xsd
share/schemas/OpenSMOG.xsd
share/schemas/bif.xsd
share/mapfiles/rigidmap
share/mapfiles/sbmMap
share/mapfiles/sbmMapExact
share/templates/SBM_AA+gaussian/AA+gaussian-noel12.b
share/templates/SBM_AA+gaussian/AA+gaussian-noel12.bif
share/templates/SBM_AA+gaussian/AA+gaussian-noel12.nb
share/templates/SBM_AA+gaussian/AA+gaussian-noel12.sif
share/templates/SBM_AA+gaussian/.citation
share/templates/SBM_calpha+gaussian/CA+gaussian-lammert09.bif
share/templates/SBM_calpha+gaussian/CA+gaussian-lammert09.b
share/templates/SBM_calpha+gaussian/CA+gaussian-lammert09.nb
share/templates/SBM_calpha+gaussian/CA+gaussian-lammert09.sif
share/templates/SBM_calpha+gaussian/.citation
share/templates/SBM_calpha/CA-clementi00.bif
share/templates/SBM_calpha/CA-clementi00.nb
share/templates/SBM_calpha/.citation
share/templates/SBM_calpha/CA-clementi00.b
share/templates/SBM_calpha/CA-clementi00.sif
share/templates/SBM_AA/AA-whitford09.b
share/templates/SBM_AA/.citation
share/templates/SBM_AA/AA-whitford09.sif
share/templates/SBM_AA/AA-whitford09.nb
share/templates/SBM_AA/AA-whitford09.bif
src/tools/SCMcode/manifest.txt
src/tools/SCMcode/org/smogserver/scm/Residue.class
src/tools/SCMcode/org/smogserver/scm/Contacts.java
src/tools/SCMcode/org/smogserver/scm/Atom.java
src/tools/SCMcode/org/smogserver/scm/GroTrajectory.class
src/tools/SCMcode/org/smogserver/scm/BondedList.java
src/tools/SCMcode/org/smogserver/scm/Topology.java
src/tools/SCMcode/org/smogserver/scm/ContactMap.class
src/tools/SCMcode/org/smogserver/scm/Contact.java
src/tools/SCMcode/org/smogserver/scm/GroTopSkinny.class
src/tools/SCMcode/org/smogserver/scm/PDBfile.class
src/tools/SCMcode/org/smogserver/scm/BondedList.class
src/tools/SCMcode/org/smogserver/scm/GroGro.class
src/tools/SCMcode/org/smogserver/scm/Structure.class
src/tools/SCMcode/org/smogserver/scm/Restype.class
src/tools/SCMcode/org/smogserver/scm/AtomList.class
src/tools/SCMcode/org/smogserver/scm/Chain.class
src/tools/SCMcode/org/smogserver/scm/Chain.java
src/tools/SCMcode/org/smogserver/scm/ContactMap.java
src/tools/SCMcode/org/smogserver/scm/Residue.java
src/tools/SCMcode/org/smogserver/scm/Contacts.class
src/tools/SCMcode/org/smogserver/scm/ShadowMain.class
src/tools/SCMcode/org/smogserver/scm/AtomList.java
src/tools/SCMcode/org/smogserver/scm/Structure.java
src/tools/SCMcode/org/smogserver/scm/ShadowMain.java
src/tools/SCMcode/org/smogserver/scm/Topology.class
src/tools/SCMcode/org/smogserver/scm/Atom.class
src/tools/SCMcode/org/smogserver/scm/ShadowSettings.java
src/tools/SCMcode/org/smogserver/scm/GroGro.java
src/tools/SCMcode/org/smogserver/scm/GroTopSkinny.java
src/tools/SCMcode/org/smogserver/scm/PDBfile.java
src/tools/SCMcode/org/smogserver/scm/Restype.java
src/tools/SCMcode/org/smogserver/scm/ShadowSettings.class
src/tools/SCMcode/org/smogserver/scm/GroTrajectory.java
src/tools/SCMcode/org/smogserver/scm/Contact.class
src/tools/SCMcode/deploy.bash
src/tools/SCM.jar
src/tools/WHAM.jar
src/tools/WHAMcode/manifest.txt
src/tools/WHAMcode/org/smogserver/wham/WhamMain.class
src/tools/WHAMcode/org/smogserver/wham/WhamMain.java
src/tools/WHAMcode/org/smogserver/wham/WhamMain$SmartBin.class
src/tools/WHAMcode/org/smogserver/wham/WhamMain$InnerThread.class
src/tools/WHAMcode/deploy.bash
src/tools/ions
src/tools/extract
src/tools/tablegen
src/tools/scale-energies
src/tools/adjustPDB
src/templateParser.pm
src/OpenSMOG.pm
src/mathFunctions.pm
src/smogv2
src/smog_common.pm
src/PDB_Bonded.pm
src/SMOGglobals.pm
src/setRatios.pm