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Fist: Fix segfault for systems without dihedrals
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| &GLOBAL | ||
| PRINT_LEVEL LOW | ||
| &END GLOBAL | ||
|
|
||
| &FORCE_EVAL | ||
| METHOD FIST | ||
| &MM | ||
| &FORCEFIELD | ||
| PARMTYPE AMBER | ||
| PARM_FILE_NAME ../sample_top/ch4.top | ||
| &END FORCEFIELD | ||
| &POISSON | ||
| &EWALD | ||
| EWALD_TYPE NONE | ||
| &END EWALD | ||
| &END POISSON | ||
| &END MM | ||
| &SUBSYS | ||
| &CELL | ||
| ABC [angstrom] 15 15 15 | ||
| ALPHA_BETA_GAMMA 90 90 90 | ||
| &END CELL | ||
| &TOPOLOGY | ||
| CONN_FILE_FORMAT AMBER | ||
| CONN_FILE_NAME ../sample_top/ch4.top | ||
| COORD_FILE_FORMAT CRD | ||
| COORD_FILE_NAME ../sample_crd/ch4.crd | ||
| &END TOPOLOGY | ||
| &END SUBSYS | ||
| &END FORCE_EVAL |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| ***** | ||
| 5 | ||
| 0.9280000 0.0600000 -0.0340000 0.5640000 0.8390000 0.6390000 | ||
| 0.5640000 0.2530000 -1.0460000 0.5640000 -0.9120000 0.3040000 | ||
| 2.0200000 0.0600000 -0.0340000 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,131 @@ | ||
| %VERSION VERSION_STAMP = V0001.000 DATE = 02/14/24 09:29:49 | ||
| %FLAG TITLE | ||
| %FORMAT(20a4) | ||
| ***** | ||
| %FLAG POINTERS | ||
| %FORMAT(10I8) | ||
| 5 2 4 0 6 0 0 0 0 0 | ||
| 11 1 0 0 0 1 1 0 2 0 | ||
| 0 0 0 0 0 0 0 0 5 0 | ||
| 0 | ||
| %FLAG ATOM_NAME | ||
| %FORMAT(20a4) | ||
| C H H1 H2 H3 | ||
| %FLAG CHARGE | ||
| %FORMAT(5E16.8) | ||
| -1.98258624E+00 4.86535410E-01 4.86535410E-01 4.86535410E-01 4.86535410E-01 | ||
| %FLAG ATOMIC_NUMBER | ||
| %FORMAT(10I8) | ||
| 6 1 1 1 1 | ||
| %FLAG MASS | ||
| %FORMAT(5E16.8) | ||
| 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 | ||
| %FLAG ATOM_TYPE_INDEX | ||
| %FORMAT(10I8) | ||
| 1 2 2 2 2 | ||
| %FLAG NUMBER_EXCLUDED_ATOMS | ||
| %FORMAT(10I8) | ||
| 4 3 2 1 1 | ||
| %FLAG NONBONDED_PARM_INDEX | ||
| %FORMAT(10I8) | ||
| 1 2 2 3 | ||
| %FLAG RESIDUE_LABEL | ||
| %FORMAT(20a4) | ||
| UNL | ||
| %FLAG RESIDUE_POINTER | ||
| %FORMAT(10I8) | ||
| 1 | ||
| %FLAG BOND_FORCE_CONSTANT | ||
| %FORMAT(5E16.8) | ||
| 3.45250000E+02 | ||
| %FLAG BOND_EQUIL_VALUE | ||
| %FORMAT(5E16.8) | ||
| 1.09620000E+00 | ||
| %FLAG ANGLE_FORCE_CONSTANT | ||
| %FORMAT(5E16.8) | ||
| 3.58000000E+01 | ||
| %FLAG ANGLE_EQUIL_VALUE | ||
| %FORMAT(5E16.8) | ||
| 1.88024401E+00 | ||
| %FLAG DIHEDRAL_FORCE_CONSTANT | ||
| %FORMAT(5E16.8) | ||
|
|
||
| %FLAG DIHEDRAL_PERIODICITY | ||
| %FORMAT(5E16.8) | ||
|
|
||
| %FLAG DIHEDRAL_PHASE | ||
| %FORMAT(5E16.8) | ||
|
|
||
| %FLAG SCEE_SCALE_FACTOR | ||
| %FORMAT(5E16.8) | ||
|
|
||
| %FLAG SCNB_SCALE_FACTOR | ||
| %FORMAT(5E16.8) | ||
|
|
||
| %FLAG SOLTY | ||
| %FORMAT(5E16.8) | ||
| 0.00000000E+00 0.00000000E+00 | ||
| %FLAG LENNARD_JONES_ACOEF | ||
| %FORMAT(5E16.8) | ||
| 1.02073671E+06 1.00235148E+05 7.94617769E+03 | ||
| %FLAG LENNARD_JONES_BCOEF | ||
| %FORMAT(5E16.8) | ||
| 6.63431737E+02 1.37787728E+02 2.57122925E+01 | ||
| %FLAG BONDS_INC_HYDROGEN | ||
| %FORMAT(10I8) | ||
| 0 3 1 0 6 1 0 9 1 0 | ||
| 12 1 | ||
| %FLAG BONDS_WITHOUT_HYDROGEN | ||
| %FORMAT(10I8) | ||
|
|
||
| %FLAG ANGLES_INC_HYDROGEN | ||
| %FORMAT(10I8) | ||
| 3 0 6 1 3 0 9 1 3 0 | ||
| 12 1 6 0 9 1 6 0 12 1 | ||
| 9 0 12 1 | ||
| %FLAG ANGLES_WITHOUT_HYDROGEN | ||
| %FORMAT(10I8) | ||
|
|
||
| %FLAG DIHEDRALS_INC_HYDROGEN | ||
| %FORMAT(10I8) | ||
|
|
||
| %FLAG DIHEDRALS_WITHOUT_HYDROGEN | ||
| %FORMAT(10I8) | ||
|
|
||
| %FLAG EXCLUDED_ATOMS_LIST | ||
| %FORMAT(10I8) | ||
| 2 3 4 5 3 4 5 4 5 5 | ||
| 0 | ||
| %FLAG HBOND_ACOEF | ||
| %FORMAT(5E16.8) | ||
|
|
||
| %FLAG HBOND_BCOEF | ||
| %FORMAT(5E16.8) | ||
|
|
||
| %FLAG HBCUT | ||
| %FORMAT(5E16.8) | ||
|
|
||
| %FLAG AMBER_ATOM_TYPE | ||
| %FORMAT(20a4) | ||
| c3 hc hc hc hc | ||
| %FLAG TREE_CHAIN_CLASSIFICATION | ||
| %FORMAT(20a4) | ||
| BLA BLA BLA BLA BLA | ||
| %FLAG JOIN_ARRAY | ||
| %FORMAT(10I8) | ||
| 0 0 0 0 0 | ||
| %FLAG IROTAT | ||
| %FORMAT(10I8) | ||
| 0 0 0 0 0 | ||
| %FLAG RADIUS_SET | ||
| %FORMAT(1a80) | ||
| modified Bondi radii (mbondi) | ||
| %FLAG RADII | ||
| %FORMAT(5E16.8) | ||
| 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 | ||
| %FLAG SCREEN | ||
| %FORMAT(5E16.8) | ||
| 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 | ||
| %FLAG IPOL | ||
| %FORMAT(1I8) | ||
| 0 |