Dear Prof. David.
Can you give me some advice on the writing of def file. I create a rigid molecule like this, but when I calaculted it, it complete with nothing output, and the pbs.err file shows that shift all potential.
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
0
0
0
#Number Of Atoms
12
# Number of groups
1
# aromatic-group
rigid
# Number of atoms
12
# atomic positions
1 Ala_O1 0.868 2.37 0.463
2 Ala_C2 0.974 0.957 0.448
3 Ala_C3 -0.36 0.225 0.23
4 Ala_O4 2.109 0.435 -0.215
5 Ala_C5 -0.232 -1.292 0.413
6 Ala_N6 -0.821 0.503 -1.162
7 Ala_H7 -1.106 0.623 0.975
8 Ala_H8 -1.22 -1.8 0.244
9 Ala_H9 0.118 -1.525 1.451
10 Ala_H10 0.518 -1.674 -0.324
11 Ala_H11 -1.778 0.048 -1.29
12 Ala_H12 -0.923 1.559 -1.246
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 11 0 0 0 0 0 0 0 0 0 0 0 0 0
# Bond stretch: atom n1-n2, type, parameters
2 1 RIGID_BOND
3 2 RIGID_BOND
4 2 RIGID_BOND
5 3 RIGID_BOND
6 3 RIGID_BOND
7 3 RIGID_BOND
8 5 RIGID_BOND
9 5 RIGID_BOND
10 5 RIGID_BOND
11 6 RIGID_BOND
12 6 RIGID_BOND
# Number of config moves
0
the information in pbs.err
read binary file
Crash set to false
read binary file
Crash set to false
_symmetry_space_group_name_H-M: P1 found space group: 1
_symmetry_Int_Tables_number: 1
space group found from symmetry elements: 1 (nr elements: 1)
_cell_length_a: 27.124000
_cell_length_b: 15.270000
_cell_length_c: 12.010000
_cell_length_alpha: 90.000000
_cell_length_beta: 94.600000
_cell_length_gamma: 90.000000
End reading cif-file
Shift all potentials
Please give me some advice on that, thank you!
