Re: [AMBER] modified potentials

From: David Cerutti <>
Date: Fri, 29 Jul 2016 10:55:31 -0400

In what way would you like to "truncate" the interaction? It is possible
to specify NBFIX-like terms in Amber (LJEDIT), either as a new section of
the parameter file (the thing that's called in order to build topologies)
or, I think, using ParmEd. These LJEDIT terms are pair-specific
Lennard-Jones interactions, so you could modify the interaction for
particular types of atoms interacting with one another. The behavior is to
leave the standard combining rules in effect unless otherwise stated, so
all other interactions between said particles would stay the same.

If the particles are few in number and always bonded to one another in
fairly close proximity, you might be able to get away with some fancy NMR
restraints that have no effect for r > L, where L is something like 4-8 A,
and for r <= L the restraints attenuate or cancel out the effect of the
Lennard-Jones terms you want to get rid of. I'd suggest trying LJEDIT


On Fri, Jul 29, 2016 at 9:52 AM, Irem Altan <> wrote:

> Hi,
> I was wondering, is it possible to use modified potentials in Amber for
> nonbonded interactions? Specifically, I would like to truncate the LJ
> potentials at the repulsive core for some protein atoms. Those atoms would
> interact with the truncated potential amongst themselves, but use the full
> form of the potential when interacting with other atoms. Is it possible to
> do this with the tools available in Amber?
> Best,
> Irem
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Received on Fri Jul 29 2016 - 08:00:02 PDT
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