[gmx-users] REMD protein-ligand separation

[David Osguthorpe]

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?

Im using gromacs 3.3.1 for the simulations for consistency with previous work
- whats the latest trjconv version I can use to see if there are trjconv fixes?

thanks

David