On Thu, Apr 13, 2017, Emilia Pecora-de-barros wrote:
>
> I'm trying to do ligand parameterization of a ligand of interest. I've
> done geometry optimization and RESP charge derivation using Gaussian
> 6-31G*, and parameters were derived using GAFF. However in the
> simulations this ligand is more flexible than expected, and even
> displays rotation of a double bond (between C1 and C2), going from a
> trans to cis conformation. The mol2 file generated is below.
Can you post the entire mol2 file, so that it can be easily visualized?
Antechamber is indeed assigning a single-bond to C1-C2 (atom types ce
and cc). There are certainly cases where the effective bond orders in
conjugated systems are not correct, and you may want/need to manually
modify either the atom types or the dihedrals involved.
....dac
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Received on Thu Apr 13 2017 - 19:00:02 PDT
