Sorry Viktor and Warren, but I don't think your suggestions are
applicable. I have only a single protein molecule in my trajectory,
which I kept centered at the origin, so it never traverses the
periodic boundary. I did strip all but 20 waters from it using ptraj
and created the appropriate
Dmitry,
is your system a single molecule or is it composed of multiple molecules
(e.g. dimer)? Amber should not 'cut' your molecule into pieces, imaging
can only separate molecules in a dimer, trimer or such. Also, was your
system solvated? Did you strip water before visualizing in PyMOL? The
Dmitry,
VMD may have the ability to shift and recombine the molecule relative to
the periodic boundary in order to avoid this dismembered effect, whereas
currently PyMOL does not. I believe ptraj can do this for you, though
it has been ages since I have tried using PyMOL with Amber.
Cheers,
Warr
