Hello everyone, I’m parametrizing the ANP-PNP molecule with FFParam. Im on the step of fitting bonded parameters. When executing the QM Bond/Angle/Dihedral PES input files with Psi4 Im getting an error when the code reaches mol=psi4.geometry(psi4_xyz) and cant figure out how to fix it.
The error is: *** qcelemental.exceptions.MoleculeFormatError: Unprocessable Molecule remnants under [psi4, xyz, xyz+, psi4+]:
And a list of atoms with their xyz positions.
The input file is called anp_bondscan_o2bpb.py
The file with the coordinates is called anp_bondscan_o2bpb_xyz.py
Both are attached.
Just to get the full error:
Traceback (most recent call last):
File "/home/leonardo/psi4conda/lib/python3.9/site-packages/qcelemental/molparse/from_string.py", line 256, in from_string
molstr, molinit = parse_as_psi4_ish(molstr, unsettled=True)
File "/home/leonardo/psi4conda/lib/python3.9/site-packages/qcelemental/molparse/from_string.py", line 217, in parse_as_psi4_ish
raise MoleculeFormatError(f"""Unprocessable Molecule remnants under {dtype}:\n{molstr}""")
qcelemental.exceptions.MoleculeFormatError: Unprocessable Molecule remnants under [psi4, xyz, xyz+, psi4+]:
O1G 1.9190901294 -4.0300203396 -3.2098481477
H1G 2.0359745025 -3.4377604413 -3.9791216236
O2G 2.4604523004 -4.5343740115 -0.8514379430
O3G 4.4541321909 -3.9597571334 -2.4846493484
H2G 3.1617103015 -5.1048957042 -0.4855489058
O1B 3.1328022703 -1.3882767619 -3.9525439118
O2B 3.9587305230 -0.2520133938 -2.2181213521
N3B 2.7155945178 -2.1206394785 -1.5904805877
H1B 3.9483075438 -1.1348248846 -4.4277091966
H3B 2.2875693624 -1.9601969296 -0.6767630109
O1A 1.5095516458 -0.0600324027 0.0973132739
O2A -0.3099242926 0.9775706016 -1.5470626055
O3A 1.7745966676 0.1260866533 -2.4810780493
O5' 1.8758876946 2.2344978183 -1.0787399106
C5' 2.1830312264 2.7969105619 0.2108347543
H2A -0.7157451604 1.6201079914 -0.9191378920
H5'1 2.4626459458 1.9986300416 0.9042903140
H5'2 3.0378304773 3.4609769458 0.0579297566
C4' 0.9815482567 3.5752306570 0.7176510538
H4' 0.8045924304 4.4582777792 0.0922657164
O4' -0.1904119785 2.7171372968 0.6197422537
C3' 1.1074429885 3.9472121582 2.1977205293
H3'1 2.1498527994 4.0121842660 2.5372973900
O3' 0.3821022744 5.1352003310 2.5195621163
H3'2 0.9036018164 5.9105772203 2.2494354293
C2' 0.3251875363 2.8311098779 2.8929754736
H2'1 0.9104522397 1.9052237769 2.9177816532
O2' -0.0645664236 3.1234120771 4.2065577056
H2'2 -0.3323115791 4.0633183178 4.2015704521
C1' -0.8352188630 2.6615582224 1.9102533776
H1' -1.5626191210 3.4754867445 2.0179824837
Im using conda 4.10.3, psi-rt 1.5, psi 1.5+e9f4d6d, qcelemental 0.24.0, python 3.9.7
The old psi4 version is needed, due to psi4 output differences in new versions and FFParam parsers.
Thank you for your time!
anp_bondscan_o2bpb.py (1.6 KB)
anp_bondscan_o2bpb_xyz.py (30.3 KB)