Author Topic: Shift all potential  (Read 13 times)

Monica_Gao

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Shift all potential
« on: April 06, 2021, 04:24:03 PM »
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!