Hello,
Hi! I am trying to run obenergy on the TERRA Quadruplex (PDB Code 3IBK) and
> I
> am having trouble getting MMFF94 force field to calculate the energy. I am
> not sure what is causing this problem (I have only basic knowledge in
> computational chemistry) and I was wondering if any of you can help me out.
>
> SETTING UP BOND CALCULATIONS...
> USING EMPIRICAL RULE FOR BOND STRETCHING 1-2 (IDX)...
> COULD NOT FIND PARAMETERS FOR BOND 58-522 (IDX)...
> obenergy: could not setup force field.
>
>
Never used obenergy, but the message seems clear to me: it cannot handle K
atoms. GAFF says the same.
Look into the pdb file: residue G 3, chain A, atom 58, is linked (see LINK
field) to K ion (line 965, atom 523, obenergy is talking about atom num.
522, because the TER line doesn't count for an atom, of course). Or at
least it is my interpretation :)
Or look at the structure (pymol) to confirm that.
My advice: delete K atoms or find o force field able to handle potassium,
or find the parameters which should be used. Using H VDW parameters is
obviously not good.
> GAFF seems to run into errors but outputs an answer:
> COULD NOT FIND VDW PARAMETERS FOR ATOM K, USING HYDROGEN VDW PARAMETERS
>
>
Regards,
Pascal
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