I am running a simple energy calculation on a conformer of 3-Sulfopropyl methacrylate, which is given my C=C(C)C(=O)OCCCS(=O)(=O)[O-]
.
This is my workflow:
- Generate conformers using genetic algorithm in OpenBabel
obabel -:"C=C(C)C(=O)OCCCS(=O)(=O)[O-]" -O SPMA.pdb --gen3D -d
obabel SPMA.pdb -O SPMA_op.xyz --conformer --nconf 300 --score rmsd --writeconformers
- Extract coordinates of conformer, and put them in psi4 input file given by:
memory 8 GB
molecule MA0 {
0 1
C 3.89733 0.15289 -1.35762
C 4.59280 1.05052 -0.63907
C 5.20105 2.27534 -1.24308
C 4.74095 0.79591 0.82319
O 5.01564 1.66100 1.64197
O 4.54800 -0.52000 1.09100
C 5.28200 -1.03600 2.21300
C 6.78400 -0.89700 2.00000
C 7.24307 -1.67225 0.77007
S 6.44265 -1.12891 -0.72122
O 6.80895 0.28345 -0.80582
O 7.02056 -1.98627 -1.75252
O 5.02989 -1.37699 -0.43672
H 3.77090 0.29082 -2.37251
H 3.48966 -0.67439 -0.89456
H 4.99668 2.29431 -2.29321
H 6.25936 2.26265 -1.08586
H 4.78246 3.14570 -0.78247
H 5.04197 -2.07085 2.34094
H 5.00988 -0.47515 3.08265
H 7.29461 -1.27505 2.86096
H 7.00956 0.13820 1.85038
H 7.02443 -2.70921 0.91770
H 8.29303 -1.50198 0.65390
H 7.75698 0.36077 -0.99601
H 7.95459 -1.75656 -1.87793
}
set {
scf_type = df
freeze_core = true
}
E, wfn = energy('HF-3c', return_wfn=True)
oeprop(wfn, 'DIPOLE', 'QUADRUPOLE', 'MULTIPOLE(4)', 'MO_EXTENTS', 'MULLIKEN_CHARGES', 'LOWDIN_CHARGES', 'WIBERG_LOWDIN_INDICES', 'MAYER_INDICES', 'NO_OCCUPATIONS', title='Methacrylic acid (MA0)')
print_variables()
- Now I run psi4 on this file:
psi4 -n 2 -i SPMA_conf.in -o SPMA.out
When I run this, however, I get a wall of error messages.
Printing out the relevant lines from the Psithon --> Python processed input file:
H 7.00956 0.13820 1.85038
H 7.02443 -2.70921 0.91770
H 8.29303 -1.50198 0.65390
H 7.75698 0.36077 -0.99601
H 7.95459 -1.75656 -1.87793
--> ""","MA0")
core.IO.set_default_namespace("MA0")
core.set_global_option("SCF_TYPE", "df")
core.set_global_option("FREEZE_CORE", "true")
E, wfn = energy('HF-3c', return_wfn=True)
oeprop(wfn, 'DIPOLE', 'QUADRUPOLE', 'MULTIPOLE(4)', 'MO_EXTENTS', 'MULLIKEN_CHARGES', 'LOWDIN_CHARGES', 'WIBERG_LOWDIN_INDICES', 'MAYER_INDICES', 'NO_OCCUPATIONS', title='Methacrylic acid (MA0)')
This seems to be the relevant portion of the error message...
I have run the very same process on other conformers of other non-charged molecules, but I have not run into this problem. Is it because 3-Sulfopropyl methacrylate is charged?
A similar problem arises when I run another charged molecule, like C=C(C)C(=O)OCC[N+](C)(C)C
.
How can I fix this problem? Any advice you have would be appreciated!
0 1
in the input file represent charge and multiplicity. the 0 represents charge, so once i change that to -1 for the first one, and +1 for the second one, it all works out. $\endgroup$