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.
--Niel
On Tue, Nov 18, 2014 at 2:20 PM, Chris Moth <cmoth08.gmail.com> 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
