I have a ligand whose original structure has =O(double bonded oxygen - keto group) attached as a functional group to the main ligand molecule.
When I optimize the geometry with PRODRG2, the group becomes -OH (hydroxyl group) in the final output structure after adding hydrogens ....
Is this normal or is it introducing an error as length of double bonds is certainly different from a single bond as also the placement of oxygen atom in space in the final structure ....?
Please provide your valuable inputs...
Thank you,
Jay.
See their FAQ regarding protonation and hybridization states.
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/prodrg_faq.html
Be sure to refine the topology after generating it. PRODRG topologies are not of sufficient quality to use without additional work.
Dear Jay M,
If this is NOT a program error, it might be that upon optimization, the tautomer, the enol form, is more stable than the keto form . I have to see the structure in order to give a precise answer.
Hoping this will be helpful,
Rafik
As mentioned above it's certainly possible that the enol form is more stable than the keto form. If you're not sure, you can always take both for further computational steps (docking or MD if I presume correctly) or use different software to predict the most likely form. Schrodinger has some nice tool to check possible protonation states with good accuracy.
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