Re: [AMBER] nmr restraints and periodic boundary conditions

From: Niel Henriksen <>
Date: Tue, 18 Nov 2014 15:02:07 -0800

Hi Chris,

I also discovered this problem just last week.

My solution, as Jason mentioned, was to image and center the molecules
which have a restraint between them

One can merge two separate residues into one "molecule" fairly easily
with ParmEd such that the molecules are imaged together by iwrap.


On Tue, Nov 18, 2014 at 2:20 PM, Chris Moth <> wrote:

> A recent simulation apparently failed because a heme group tethered to a
> histindine residue (via nmr bond restraint) was wrapped into a different
> periodic cell from the histidine. When the following pmemd simulation
> segment started, the "nmr bond" term spiked to several thousand Kcal,
> and protein structure was badly contorted as energy re-equilibrated.
> There is scattered information on this kind of problem in the amber
> reflector, but I'd greatly appreciate a quick update in context of
> Amber14, before I attempt to modify some of the PMEMD source code to
> work around the trouble.
> 1) Do you agree that the nmr_lib.F90 disrng() function does not consider
> periodic images in its nmr restraint calculation energy?
> 2) Do you agree that wrap_to() in pbc.F90 could be modified so that the
> "center of mass" of the tethering protein could be used to move the heme
> group along with it? Slightly Rephrased... Is there any harm in
> skipping the COM calculation of the heme group, and just wrapping it by
> using the COM of the tethering protein?
> 3) Is there a restraint solution that replaces NMR bond restraints and
> handles differing simulation cell spanning correctly?
> 4) Why isn't this more of a routine problem for others in the Amber
> community?
> 5) I suppose one could build a combination histindine+heme residue and
> use that at the position that is causing trouble. But, that feels
> awkward. Any other advice?
> Thanks
> Chris
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Received on Tue Nov 18 2014 - 15:30:02 PST
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