AMBER Archive (2007)

Subject: Re: AMBER: LJ potential

From: David A. Case (case_at_scripps.edu)
Date: Sat Jan 27 2007 - 12:03:15 CST

On Wed, Jan 24, 2007, Steve Seibold wrote:
>
> I am using AMBER8 and I am attempting to "mimic" a covalent bond between
> two atoms (not creating new atom types). I am using nmr restraints
> (NMROPT>1), but I believe this is similar to NTR=1 in the sense that
> they are positional restraints using external force. Correct? Is there a
> way to use a LJ potential (make the well deeper; episilon factor
> greater?) Is this the &wt=ATTRACT weight term?
>

The nmr restraints are like harmonic bond terms; if you set ialtd=1, you
can get something that goes to a constant at large distances, more like a
Lennard-Jones potential. But this is only a rough analogy: if you want LJ
interactions whose strength you can vary, you need to define new atom types.

...regards....dac
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