Re: [AMBER] Problem with lone pair

From: Jason Swails <>
Date: Tue, 14 Oct 2014 17:37:17 -0400

On Mon, Oct 13, 2014 at 4:23 AM, Giachetti Andrea - CERM <> wrote:

> Dear all,
> I'm trying to create a special residue containing a metal with three
> dummy atoms (lone pairs) to define the axes of a tensor, for use with
> paramagnetic pseudocontact shifts.
> I have created a lib file with tleap using the TNS.cmd and defined the
> parameter in TNS.par (attached).
> When I try to heat the protein (tensOK.pdb) and run an MD trajectory the
> new residue TNS remain frozen in the space. I'm using pmemd (version 14)
> compiled with cuda.
> Can you think of a possible error I am making?

​Yes, the dummy atoms you've added have a mass of 0. Amber integrates
classical equations of motion according to Newton's laws: F=ma. Those laws
don't work with massless particles :).

​Lone pairs are typically represented with extra points instead, which are
​massless particles that are handled as "extensions" of the atom (or atoms)
they are attached to (such that their forces and torques are transferred to
the "actual" particles defined in their frame).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 14 2014 - 15:00:02 PDT
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