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 - 14:30:02 PST
