On Sat, Apr 30, 2016, Brett wrote:
>
> Is the files for ligand md produced by antechamber highly reliable? Or I
> still need check the files by naked eye?
Depends. We often use antechamber files in "virtual screening" mode, where
we live with whatever results we get, which are usually good, but not always
so.
If you have a single ligand that you are particularly interested in, it is
still wise to examine the files by hand, and to run some ligand-only
simulations to ensure that you are getting behavior that you can live with.
If you have even more time, you can run quantum chemical calculations, and use
programs like mdgx or paramfit to generate force fields tailored to your
particular situation.
...dac
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Received on Sat Apr 30 2016 - 05:30:03 PDT
