if I convert a structure from SMILES with molconvert to a 3D format such as mol2, pdb... does molconvert also compute the partial charges automatically? If yes, which method does it use, and does it use the charge plugin?
Yes, molconvert automatically calculates the partial charges when converting to those mentioned formats, e.g. mol2. The applied method of calculation is the same as in the Charge Plugin, which is Gasteiger's partial charge calculation algorithm.
You can find detailed description of this here:
I hope this helps.
thank you very much for your answer.
I tried it. It works with the mol2 format. But with the pdb format it doesn't add the partial charges. But pdb is also able to store partial charges. Is there a way to enable the partial charges for the pdb format?
No, unfortunately molconvert is not able to generate pdb files with partial charges at the moment. You can only use the mol2 file format for that.