Problems when using EMC building molecule with PCFF

EMC
1

Dear,
when I tried to build molecule like as below with PCFF, EMC gives tips :
Warning: increment pair {o_2, c-} set to zero.
Warning: increment pair {c-, na} set to zero.
Warning: no torsion coefficients found for {hc, c, o_2, c-}.
Warning: no torsion coefficients found for {c, c, o_2, c-}.

image
image934×354 7.39 KB

Missing force field parameters.
Program aborted.

smiles: [H]C([H])(O)C([H])([H])C([H])([H])C([H])([H])OC(=O)Nc2ccc(C([H])([H])c1ccc(N)cc1)cc2

How to solve this problem? thank you.
Tony

2

Dear user,

Thank you for reporting the above issue. The problem stems from incorrect typing of the carbamate carbonyl carbon. This can be remedied by adding the following to your pcff_templates.dat file:

type:c_2
    ! carbamate, urea carbonyl carbon
    template: (>C (=O) (~N) (~O))
    atom_test:1
        hybridization:sp2
    end_test
end_type

which can be found at $EMC_ROOT/field/pcff/pcff_templates.dat. For your convenience, I am including this file here:

pcff_templates.dat (38.5 KB)

Please note that one does not need to include explicit hydrogens in the SMILES definition for stereochemically non-specific molecules:

C(O)CCCOC(=O)Nc2ccc(Cc1ccc(N)cc1)cc2

I used the following script to build this molecule:

setup.esh (472 Bytes)

3

Thanks a lot for your replying. :grinning: :grinning:

Tony