Dear Q-Chem specialists!
I tried to perform geometry optimization calculations using user-defined force field (as in chapter 11.3.2.3 of Q-Chem manual). Unfortunately, I am getting segmentation fault.
Here is what I did:
Step 1.: I used prof. Jorgensen’s LigParGen server to generate OPLS parameters for the uracil molecule using its SMILES code.
Step 2.: I found the *.prm file inside the package.
Step 3.: I modified it accordingly to Q-Chem manual
Step 4.: I prepared input file and I am getting segmentation fault…
So here is my input file:
$rem
JOBTYPE OPT
GEOM_OPT_MAX_CYCLES 1000
FORCE_FIELD READ
USER_CONNECT TRUE
$end
$molecule
0 1
N 0.00500 0.71700 1.16300 1 3 4 7 0
N -0.00000 2.71600 0.00000 3 8 4 5 0
H -0.06500 0.23400 2.06500 7 1 0 0 0
C 0.02500 2.08500 1.21200 2 1 2 11 0
C -0.02600 2.09100 -1.21400 4 2 12 6 0
C 0.00200 0.61400 -1.18500 5 5 7 9 0
C 0.00000 0.00000 0.00000 6 1 10 6 0
H -0.07000 3.72700 0.02500 9 2 0 0 0
H -0.00900 0.08700 -2.12800 11 6 0 0 0
H -0.01500 -1.08000 0.10100 12 7 0 0 0
O 0.04300 2.70900 2.27000 8 4 0 0 0
O -0.08600 2.69900 -2.28100 10 5 0 0 0
$end
$force_field_params
Filename /net/people/plgzonkil9/params_plg.prm
$end
And here is my force field parameters file:
//-- Force Field Example --//
// – Rules – //
RadiusRule Geometric
RadiusSize Diameter
EpsilonRule Geometric
ImptorType Trigonometric
vdw-14-scale 2.0
chg-14-scale 2.0
torsion-scale 0.5
NAtom 12
Nvdv 6
// – Atoms – //
Atom 1 -0.60 1 N1
Atom 2 0.50 2 C2
Atom 3 -0.51 1 N3
Atom 4 0.45 2 C4
Atom 5 -0.07 3 C5
Atom 6 0.08 3 C6
Atom 7 0.41 4 H-N1
Atom 8 -0.40 5 O-C2
Atom 9 0.36 4 H-N3
Atom 10 -0.42 5 O-C4
Atom 11 0.10 6 H-C5
Atom 12 0.10 6 H-C6
// – vdw – //
vdv 1 3.25 0.170
vdv 2 3.75 0.105
vdv 3 3.50 0.080
vdv 4 0.00 0.000
vdv 5 2.96 0.210
vdv 6 2.50 0.050
// – Bond – //
Bond 2 5 1140.0 1.2290
Bond 1 2 836.0 1.3880
Bond 3 1 896.0 1.3650
Bond 3 3 1098.0 1.3400
Bond 2 3 820.0 1.4440
Bond 4 1 868.0 1.0100
Bond 6 3 734.0 1.0800
// – Angle – //
Angle 5 2 1 160.0 120.60
Angle 2 1 3 140.0 121.60
Angle 1 3 3 140.0 121.20
Angle 3 3 2 170.0 120.70
Angle 3 2 5 160.0 125.30
Angle 1 3 6 70.0 120.00
Angle 2 1 4 70.0 116.80
Angle 3 2 1 140.0 114.10
Angle 3 1 4 70.0 119.20
Angle 2 1 2 140.0 126.40
Angle 3 3 6 70.0 120.00
Angle 2 3 6 70.0 120.00
Angle 1 2 1 140.0 118.60
// – Torsion – //
Torsion 3 1 2 5 3.04450 180.00000 1
Torsion 3 3 1 2 0.00000 0.00000 1
Torsion 2 3 3 1 7.00000 180.00000 1
Torsion 5 2 3 3 3.00000 180.00000 1
Torsion 6 3 1 4 5.00000 180.00000 1
Torsion 1 2 1 3 3.62500 180.00000 1
Torsion 6 3 1 2 0.00000 0.00000 1
Torsion 2 1 2 5 2.45000 180.00000 1
Torsion 4 1 2 3 2.45000 180.00000 1
Torsion 4 1 2 5 2.45000 180.00000 1
Torsion 1 2 3 3 1.00000 0.00000 1
Torsion 6 3 3 1 3.62500 180.00000 1
Torsion 3 2 1 2 0.00000 0.00000 1
Torsion 6 3 2 1 0.00000 0.00000 1
Torsion 4 1 2 5 2.45000 180.00000 1
Torsion 4 1 2 1 2.45000 180.00000 1
Torsion 6 3 2 5 0.00000 0.00000 1
Torsion 6 3 3 2 7.00000 180.00000 1
Torsion 5 2 1 2 2.45000 180.00000 1
Torsion 6 3 3 6 7.00000 180.00000 1
Torsion 4 1 3 3 2.45000 180.00000 1
Torsion 2 1 2 1 3.04450 180.00000 1
// – Improper – //
Improper 1 2 5 1 10.50000 180.00000 1
Improper 4 1 2 3 2.50000 180.00000 1
Improper 6 3 1 3 2.50000 180.00000 1
Improper 6 3 3 2 2.50000 180.00000 1
Improper 4 1 2 2 2.50000 180.00000 1
Improper 1 2 3 5 10.50000 180.00000 1
I feel that the problem is related to my *.prm file… Something with keywords? I don’t know.
I also tried to perform test calculations using the TIP3P water example in the Q-Chem manual and it ran smoothly.
Can somebody help me with my struggle?