Re: [AMBER] Side chain and backbone-specific parameters.

From: Jason Swails <>
Date: Tue, 10 Jun 2014 13:46:32 -0400

On Tue, 2014-06-10 at 10:25 -0700, Lee-Ping Wang wrote:
> Hi everyone,
> I'm working on some new protein force fields which have distinct backbone /
> sidechain parameters for different amino acids. My parameterizations are
> done using Gromacs, which allows atom-specific bonded interactions (i.e.
> overriding the values that come from atom classes).
> I don't see this functionality in AMBER, and it looks like the ff99sb-ildn
> and ff12sb models have extra atom classes to accommodate the extra torsions.
> Since I plan to port my force fields to AMBER, I'd like your advice on how
> to do this most effectively.
> What is the best way to implement residue-specific backbone and side chain
> parameters? Should this be done by adding many atom classes?


> Is it even
> possible to add on the order of 100 atom classes?

Yes. tleap should create a condensed set of vdW atom classes by
combining atoms that have the same vdW parameters into a single class,
but should have no problems handling a very large number of atom classes
for parameter assignment.

Indeed, loading the ff14SB force field with GLYCAM, lipid14, and GAFF
force fields loads ~200 atom types already.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 10 2014 - 11:00:03 PDT
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