Re: [AMBER] Small molecules paramters

From: Gustavo Seabra <>
Date: Fri, 29 May 2020 12:20:56 -0400

Although it is possible to convert parameters to AMBER *format*, so they
can be read by AMBER, this is not the ideal. Bear in mind that the MD force
fields rely on a fine balance between charges and force constants
obtained from multiple calculations, and that each force field "flavor"
uses a different methodology to obtain those parameters. So, ideally, you
will want to use for your small molecule the same methodology that was used
to derive parameters for the rest of the system, or at least have some
indication that the parameters are compatible. GAFF (ad GAFF2) have been
developed with that in mind, so their parameters are, in principle,
compatible with the Amber force fields. If you get the parameters from
other sources, make sure you do some extra testing.

All the best,
Gustavo Seabra.
On Thu, May 28, 2020 at 8:47 AM Athena N <> wrote:
> Hi all,
> I want to know if it advisable to use any other force fields than gaff for
> small molecules like some indole and pyridine systems.? If we generate some
> parameters using fftk (force field tool kit), could we use those and do the
> simulation in AMBER?
> Thank you all
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Received on Fri May 29 2020 - 09:30:02 PDT
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