[gmx-users] trjconv reference structure (bug?)

[Mikko Huhtala]

I am trying to superpose trajectories to a reference protein crystal
structure. The crystal structure is slightly different from the
simulation starting structure, so I just converted the pdb to gro but
did not solvate or add counterions etc. Thus the reference gro only
has protein atoms and the trajectory has everything. When I give the
name of the reference gro to trjconv with -s, trjconv starts, asks for
lsq fit and output groups and then does nothing. The program never
finishes and the size of the output trajectory file is 0. If I use an
artificial reference gro file into which solvent etc. has been pasted
after the protein crystal structure, trjconv -fit seems to
work. Preparing the reference structure like this is not a big
problem, just a pain in the fundament. (I am using precompiled Gromacs
3.1.4 from the rpm package on Linux.)

Mikko