[gmx-users] REMD protein-ligand separation
david.osguthorpe at gmail.com
Wed Jan 7 17:43:54 CET 2009
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?
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