David Osguthorpe wrote:
Hi,
I have performed a REMD simulation of a protein and ligand in water
as usual the protein and ligand get separated by symmetry operations
however attempts to fix this using trjconv and the standard recipes
(eg. -pbc whole, -pbc nojump) do not appear to be working
in particular after using -pbc nojump and attempting RMS -fit rot+trans
I get warning messages
....
There were 26 inconsistent shifts. Check your topology
Will stop reporting inconsistent shifts
(no such errors appear in the REMD logs)
is there any way to get the protein and ligand to be together?
There is some experience under 3.3.x that multi-stage trjconv is more
effective than one-stage trjconv. I don't recall any details, but you
may find some if you search the mailing list.
Mark
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