[gmx-users] REMD protein-ligand separation

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 7 20:55:19 CET 2009

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.


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