No VDW interaction for my made up forcefield files.

[alice]

Hello people, so I am working on MOFs adsoprtion on CO2 but the issues lies that the forcefield file which I made by taking UFF/Dreiding and OPLS Parameters is giving me no vdw warnings. For an example, check my cubtc test files: cif file portion
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_charge
Cu1  Cu     0.2853 0.2853 0.0000  1.248
O1   O_MOF  0.3166 0.2431 0.9478 -0.624
C1   C_MOF  0.2968 0.2032 0.9313  0.494
C2   C_MOF  0.3220 0.1780 0.8870  0.130
C3   C_MOF  0.3655 0.1994 0.8655 -0.156
H1   H_MOF  0.3802 0.2280 0.8802  0.156

forcefield mixing:# general rule for shifted vs truncated
truncated
# general rule tailcorrections
no
# number of defined interactions
33
# type interaction
O_CO2        lennard-jones   79.0     3.05
C_CO2        lennard-jones   27.0     2.80
Cu           lennard-jones   2.5161   3.11369
C_MOF        lennard-jones   47.8562  3.47299
O_MOF        lennard-jones   48.1581  3.03315
H_MOF        lennard-jones   7.64893  2.84642
N_BMIM       lennard-jones   85.55    3.25
C_BMIM_CR    lennard-jones   35.22    3.55
C_BMIM_CW    lennard-jones   35.22    3.55
H_BMIM_HR    lennard-jones   15.10    2.42
H_BMIM_HW    lennard-jones   15.10    2.42
C_BMIM_CM    lennard-jones   33.21    3.50
H_BMIM_HM    lennard-jones   15.10    2.50
C_BMIM_CA    lennard-jones   33.21    3.50
H_BMIM_HA    lennard-jones   15.10    2.50
C_BMIM_CS    lennard-jones   33.21    3.50
H_BMIM_HS    lennard-jones   15.10    2.50
C_BMIM_CT    lennard-jones   33.21    3.50
H_BMIM_HT    lennard-jones   15.10    2.50
B_BF4        lennard-jones   47.81    3.581
F_BF4        lennard-jones   30.70    3.118
OwH2O_TIP4P  lennard-jones   78.0     3.154
HwH2O_TIP4P  none
MwH2O_TIP4P  none
OwH2O_TIP4PEW lennard-jones  81.9     3.164
HwH2O_TIP4PEW none
MwH2O_TIP4PEW none
OwH2O_TIP5P  lennard-jones   80.52    3.12
HwH2O_TIP5P  none
MwH2O_TIP5P  none
OwH2O_TIP5PEW lennard-jones  89.57    3.097
HwH2O_TIP5PEW none
MwH2O_TIP5PEW none
# general mixing rule for Lennard-Jones
Lorentz-Berthelot

pseudo atoms def
#number of pseudo atoms
33
#type      print   as    chem  oxidation   mass        charge   polarization B-factor radii  connectivity anisotropic anisotropic-type   tinker-type
O_CO2    yes O  O  0 15.9996 -0.350  0.0 1.0 1.0 1 0 absolute 0
C_CO2    yes C  C  0 12.0110  0.700  0.0 1.0 1.0 2 0 absolute 0
Cu       yes Cu Cu 0 63.5460  0.8360  0.0 1.0 1.0 5 0 absolute 0
C_MOF    yes C  C  0 12.0110  0.4170  0.0 1.0 1.0 3 0 absolute 0
O_MOF    yes O  O  0 15.9996 -0.8340  0.0 1.0 1.0 3 0 absolute 0
H_MOF    yes H  H  0 1.0080   0.4170  0.0 1.0 1.0 1 0 absolute 0
N_BMIM   yes N  N  0 14.0070  0.1760  0.0 1.0 1.0 3 0 absolute 0
C_BMIM_CR yes C C  0 12.0110 -0.0720  0.0 1.0 1.0 3 0 absolute 0
C_BMIM_CW yes C C  0 12.0110 -0.1920  0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HR yes H H  0 1.0080   0.1680  0.0 1.0 1.0 1 0 absolute 0
H_BMIM_HW yes H H  0 1.0080   0.2160  0.0 1.0 1.0 1 0 absolute 0
C_BMIM_CM yes C C  0 12.0110 -0.2800  0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HM yes H H  0 1.0080   0.1440  0.0 1.0 1.0 1 0 absolute 0
C_BMIM_CA yes C C  0 12.0110 -0.1360  0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HA yes H H  0 1.0080   0.1440  0.0 1.0 1.0 1 0 absolute 0
C_BMIM_CS yes C C  0 12.0110 -0.0960  0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HS yes H H  0 1.0080   0.0480  0.0 1.0 1.0 1 0 absolute 0
C_BMIM_CT yes C C  0 12.0110 -0.1920  0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HT yes H H  0 1.0080   0.0640  0.0 1.0 1.0 1 0 absolute 0
B_BF4    yes B  B  0 10.8110  1.1340  0.0 1.0 1.0 3 0 absolute 0
F_BF4    yes F  F  0 18.9980 -0.5335  0.0 1.0 1.0 1 0 absolute 0
OwH2O_TIP4P yes O O 0 15.9996 0.0000 0.0 1.0 1.0 3 0 absolute 0
HwH2O_TIP4P yes H H 0 1.0008  0.5200 0.0 1.0 1.0 1 0 absolute 0
MwH2O_TIP4P yes M - 0 0.0000 -1.0400 0.0 1.0 1.0 1 0 absolute 0
OwH2O_TIP4PEW yes O O 0 15.9996 0.0000 0.0 1.0 1.0 3 0 absolute 0
HwH2O_TIP4PEW yes H H 0 1.0008  0.52422 0.0 1.0 1.0 1 0 absolute 0
MwH2O_TIP4PEW yes M - 0 0.0000 -1.04844 0.0 1.0 1.0 1 0 absolute 0
OwH2O_TIP5P yes O O 0 15.9996 0.0000 0.0 1.0 1.0 3 0 absolute 0
HwH2O_TIP5P yes H H 0 1.0008  0.2410 0.0 1.0 1.0 1 0 absolute 0
MwH2O_TIP5P yes M - 0 0.0000 -0.2410 0.0 1.0 1.0 1 0 absolute 0
OwH2O_TIP5PEW yes O O 0 15.9996 0.0000 0.0 1.0 1.0 3 0 absolute 0
HwH2O_TIP5PEW yes H H 0 1.0008  0.2410 0.0 1.0 1.0 1 0 absolute 0
MwH2O_TIP5PEW yes M - 0 0.0000 -0.2410 0.0 1.0 1.0 1 0 absolute 0

and in output getting:
WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION O_CO2-Cu1 O_CO2-O1 O_CO2-C1 O_CO2-C2 O_CO2-C3 O_CO2-H1 C_CO2-Cu1 C_CO2-O1 C_CO2-C1 C_CO2-C2 C_CO2-C3 C_CO2-H1 Cu1-O_CO2 Cu1-C_CO2 Cu1-O1 Cu1-C1 Cu1-C2 Cu1-C3 Cu1-H1 O1-O_CO2 O1-C_CO2 O1-Cu1 O1-C1 O1-C2 O1-C3 O1-H1 C1-O_CO2 C1-C_CO2 C1-Cu1 C1-O1 C1-C2 C1-C3 C1-H1 C2-O_CO2 C2-C_CO2 C2-Cu1 C2-O1 C2-C1 C2-C3 C2-H1 C3-O_CO2 C3-C_CO2 C3-Cu1 C3-O1 C3-C1 C3-C2 C3-H1 H1-O_CO2 H1-C_CO2 H1-Cu1  (maximum 50 interactions shown)


I will be working on many mofs so assigning each one a charge might not be efficient. I am using no charges from cif file itself as modifying many MOFs with ILs liquid and such reduces the charges to zero with conversions.

[dubbelda]

The warning is not that UFF/DREIDING/OPLS are incomplete. RASPA2 never matched your framework atoms to the types in the force field, so CO2 has no van der Waals interaction with the MOF. The results are not usable until this is fixed. Do not silence those pairs with "none".

RASPA2 takes the force-field type from _atom_site_label, not from _atom_site_type_symbol. Your CIF is:

Cu1  Cu     ...
O1   O_MOF  ...
C1   C_MOF  ...

so the types RASPA actually uses are Cu1, O1, C1, C2, C3, H1. That is exactly what the warning prints (O_CO2-Cu1, O_CO2-O1, ...). The mixing-rule types Cu, C_MOF, O_MOF, H_MOF are never applied. Unknown CIF labels are added as new pseudo-atoms with no Lennard-Jones parameters (and, if UseChargesFromCIFFile is no, charge 0). Check the pseudo-atom table in the output: you will see Cu1, O1, C1 listed separately from Cu, O_MOF, C_MOF.

You do not need a unique charge on every atom of every MOF. For a typed UFF/DREIDING-style model, give each chemical type one epsilon, sigma, and charge in pseudo_atoms.def / force_field_mixing_rules.def, then make the CIF labels match those type names. UseChargesFromCIFFile no is the right choice if conversion to IL-modified structures is wiping _atom_site_charge.

Two practical ways to make the names match, depending on how you generate CIFs.

1. Keep C_MOF / O_MOF / H_MOF / Cu in the force field (good if you want MOF atoms distinct from CO2, water, and the IL). Rewrite the CIF labels to those names. Labels do not have to be unique:

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Cu     Cu  0.2853 0.2853 0.0000
O_MOF  O   0.3166 0.2431 0.9478
C_MOF  C   0.2968 0.2032 0.9313
H_MOF  H   0.3802 0.2280 0.8802

Keep O_CO2 and C_CO2 only for the guest.

2. Better for many CoRE-style CIFs that already use Cu1, O1, C1, C2. Rename the framework types in the force field to Cu, O, C, H and put this in simulation.input:

RemoveAtomNumberCodeFromLabel yes

That maps Cu1 → Cu, O1 → O, C1/C2/C3 → C, H1 → H. Leave the guests as O_CO2 / C_CO2 so they do not collide with framework O and C. Do not use RemoveAtomNumberCodeFromLabel with types named O_MOF: O1 becomes O, which still will not match O_MOF.

After the names match, the warning should disappear for CO2–framework pairs. Framework–framework missing VDW (Cu–O, C–H, ...) is normal for a rigid framework and can be left undefined, or listed as none if you want a clean log.

Charges for high-throughput: one charge per type in pseudo_atoms.def is enough; you do not assign a charge per MOF. UseChargesFromCIFFile no. Make sure every framework type you actually use is in pseudo_atoms.def, otherwise RASPA adds it with charge 0. The CIF charges you showed (Cu 1.248, O −0.624, ...) are not the same as the pseudo_atoms.def values (Cu 0.836, O_MOF −0.834, C_MOF 0.417, H_MOF 0.417). Pick one consistent set. H_MOF = 0.417 looking identical to C_MOF is worth checking; that is not a typical DREIDING hydrogen charge.

Also fix the mixing-rules header. RASPA2 expects:

# general rule for shifted vs truncated
shifted no
# general rule tailcorrections
no

not the word "truncated" on its own.

Once types match, confirm in the output that (1) the warning is gone for O_CO2/C_CO2 vs Cu/C/O/H, (2) the framework net charge is what you expect, and (3) Movies/System_0/Framework_0_initial_P1.cif has the charges you intended. Mixing UFF/DREIDING (framework), OPLS (IL), and TraPPE-style CO2 is then a force-field choice: Lorentz–Berthelot will run, but Cu-BTC open-metal-site CO2 uptake is often still low with generic Cu parameters. That is a separate issue from this warning.