add cofactor example as a cookbook #284
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Maybe its worth adding a note that we will be using pre-charged ligands here and pointing to the charge-molecules CLI docs for more info on how to generate these files?
I would also add a warning box highlighting that supplying cofactors this way means they are parameterised using the small molecule force field, I am not sure if its also worth highlighting how a different force field could be used or if that would confuse things.
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Line #4. offmol.assign_partial_charges('am1bcc')
This is no longer needed as the charges are in the SDF file.
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jthorton
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A few minor changes, but overall this looks great, thanks for finishing it after many years!
continuation of #91 - making a new PR to not spam everyone tagged there.