Dear Sir/Madam,
I am a grad student from the University of Georgia. I am trying to reproduce the data using the tutorial code for p450. But I have received error, but I haven’t change anything,
I just copy the whole qmmm folder which has 1_solvation and 2_qmmm folders. I am stuck with the single point calculation. I would be grateful if anyone kindly help me to resolve this issue. Here I have attached the error text for your reference:
chemsh-py-25.0.0/bin/gnu/chemsh.x -dbg 0 p450_qmmm_sp_with_psf1.py
======================================================================
Py-ChemShell 2025 (version 25.0.0)
Fri Jan 2 18:39:02 2026
Compiler gnu; Python 3.11.3; Numpy 1.26.4
Debug level 0
Please cite Py-ChemShell as:
Y. Lu, M.R. Farrow, P. Fayon, A.J. Logsdail, A.A. Sokol, C.R.A.
Catlow, P. Sherwood, and T.W. Keal, J. Chem. Theory Comput. 2019,
15, 1317-1328.
www.chemshell.org
Checking segments connectivity and contiguousness…
Time used for calculating connectivity: 0.816 s
Time used for calculating non-bond-connected fragments: 0.226 s
Residues (chain:seg:res) merged into segments according to
connectivity:
A:PROT:HEMB405 → A:HEM_:HEMB2
A:HEM_:O21 → A:PROT:O2405
A:HEM_:HEMB2 → A:PROT:HEMB406
NB: 1 duplicate resIDs reassigned for segment “PROT” chain “A”
atoms 11239 - 11239: HEMB 406 → 407
Summary of loaded fragment
Filename: p450_w_water_shell_psf.pqr
Number of atoms: 18055
Segments and residue names contained:
chain A
CAM_: CAM
CW_A: TIP3
PROT: ALA ARG ASN ASP CYS GLN GLU GLY HEMB HSD HSE ILE LEU LYS MET
O2 PHE PRO SER SOD THR TRP TYR VAL
chain W
SOLA: TIP3
SOLB: SOD TIP3
SOLC: SOD TIP3
SOLD: SOD TIP3
SOLE: TIP3
SOLF: TIP3
SOLG: SOD TIP3
SOLH: SOD TIP3
SOLI: TIP3
Assigning types data from PSF…
Time used for calculating connectivity: 0.798 s
To visualise the selection in VMD, copy the following clause and
paste to the VMD “Selected Atoms” field:
index 5445 or index 5446 or index 5447 or index 5448
“qm_region.pdb” saved.
Given QM charge value -1.0000000000000002 rounded to -1
Parsing CHARMM parameter file:
../1_solvation/camphor.prm
Indices of QM atoms:
5445 5446 5447 5448 6355 6356 6357 6358 6359 6360 6361 6362 6363 6364
6365 6366 6367 6368 6369 6370 6371 6372 6373 6374 6375 6376 6377 6378
6379 6380 6381 6382 6383 6384 6385
NB: Py-ChemShell atom indices count from 0 (cf. 1 in Tcl-ChemShell)
Assigning types data from PSF…
Assigning residues data from PSF…
Assigning resIDs data from PSF…
Assigning segments data from PSF…
Running single point calculation…
Assigning types data from PSF…
Assigning residues data from PSF…
Assigning resIDs data from PSF…
Assigning segments data from PSF…
======================================================================
ChemShell QM/MM Driver
QM/MM scheme : additive
Embedding method : electrostatic
Coupling method : covalent
QM theory : ORCA
MM theory : DL_POLY
Number of atoms : 18055
Number of QM atoms: 44 (incl. 9 link atoms)
Number of MM atoms: 18055
QM charge : -1
±------------------------------+
| ChemShell/DL_POLY Interface |
±------------------------------+
ChemShell/DL_POLY: Generating forcefield from DL_FIELD driver…
Peak memory used by procedure chemsh.interfaces.dl_field.getInpBuff: 277.375 MB
±-------------------------------+
| |
| ChemShell/DL_FIELD Interface |
| |
±-------------------------------+
Time used for calculating connectivity: 0.788 s
Time used for calculating connectivity: 0.795 s
Time used for calculating connectivity: 0.789 s
“_patched.pdb” saved.
“_patched.pqr” saved.
NB: UDFF filename for writing defaulted to _dl_field.udff
ChemShell/DL_FIELD: molecule key for interconnecting “HEMB” → “-HEMB-”
ChemShell/DL_FIELD: molecule key for interconnecting “TIP3” → “-TIP3-”
Writing out merged DL_FIELD and supplimented ChemShell data to:
_dl_field.udff
“_dl_field.udff” saved.
Residues (i.e. DL_FIELD molecule types) not found:
O2
Supplemented ChemShell/CHARMM RTF/PRM files for residue “O2”:
/home/au80451/apps/chemsh-py-25.0.0/chemsh/data/charmm/ligands.rtf
/home/au80451/apps/chemsh-py-25.0.0/chemsh/data/charmm/haems-ligands.prm
Parsing CHARMM parameter file:
/home/au80451/apps/chemsh-py-25.0.0/chemsh/data/charmm/haems-ligands.prm
ChemShell/DL_FIELD: molecule key for interconnecting “HEMB” → “-HEMB-”
ChemShell/DL_FIELD: molecule key for interconnecting “O2” → “-O2-”
ChemShell/DL_FIELD: molecule key for interconnecting “TIP3” → “-TIP3-”
Writing out merged DL_FIELD and supplimented ChemShell data to:
_dl_field.udff
“_dl_field.udff” saved.
Time used for calculating connectivity: 0.780 s
Time used for calculating connectivity: 0.773 s
Time used for calculating connectivity: 0.778 s
“_dl_field.pdb” saved.
ChemShell/DL_FIELD QM/MM treatments
QM atoms:
5445, 5446, 5447, 5448, 6355, 6356, 6357, 6358,
6359, 6360, 6361, 6362, 6363, 6364, 6365, 6366,
6367, 6368, 6369, 6370, 6371, 6372, 6373, 6374,
6375, 6376, 6377, 6378, 6379, 6380, 6381, 6382,
6383, 6384, 6385
QM-MM interactions to exclude about QM/MM junction (QM-JQ-MM):
5446 - 5443
5447 - 5443
5448 - 5443
6362 - 6390
6364 - 6390
6363 - 6386
6365 - 6386
6366 - 6399
6368 - 6399
6367 - 6403
6369 - 6403
6370 - 6408
6372 - 6408
6371 - 6412
6373 - 6412
6374 - 6417
6376 - 6417
6375 - 6421
6377 - 6421
DL_FIELD 4.12
Chin W. Yong, STFC (May 2025)
DL_FIELD Control file title:
Py-ChemShell interface to DL_FIELD v4.8
Molecular Group summary:
Group 1 number of different residue: 382 total atoms: 6430
Group 2 number of different residue: 1 total atoms: 27 residue: CAM
Group 3 number of different residue: 1 total atoms: 828 residue: TIP3
Group 4 number of different residue: 1 total atoms: 456 residue: TIP3
Group 5 number of different residue: 3 total atoms: 718
Group 6 number of different residue: 3 total atoms: 940
Group 7 number of different residue: 3 total atoms: 1840
Group 8 number of different residue: 1 total atoms: 1 residue: SOD
Group 9 number of different residue: 1 total atoms: 78 residue: TIP3
Group 10 number of different residue: 1 total atoms: 288 residue: TIP3
Group 11 number of different residue: 1 total atoms: 1245 residue: TIP3
Group 12 number of different residue: 3 total atoms: 1102
Group 13 number of different residue: 3 total atoms: 2032
Group 14 number of different residue: 1 total atoms: 2070 residue: TIP3
Set up information for POTENTIAL charmm36_prot
Error: Cannot locate MOLECULE_KEY O2 from the library file (For charmm36_prot).
If you are using PDB file, did you mistype the residue label in the file?
Are you using the correct FF scheme?
If this is a new molecule, you must create a new template MOLECULE in a udff file.
If you have done so, DL_FIELD needs to know the udff file name.
Error: Cannot locate MOLECULE_KEY CAM from the library file (For charmm36_prot).
If you are using PDB file, did you mistype the residue label in the file?
Are you using the correct FF scheme?
If this is a new molecule, you must create a new template MOLECULE in a udff file.
If you have done so, DL_FIELD needs to know the udff file name.
Error: The residue CAM in Molecular Group CAM is not available in the Molecule database.
New MOLECULE can be defined using MOLECULE directive in UDFF file.
Remember to specify the UDFF filename.Serial run failed. Exiting…
Exit code: 1