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

[Erik Lindahl]

Mikko Huhtala wrote:

>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
>
Hi Mikko,

The easiest way is usually to use the .tpr file as the reference 
structure, since it
containts both atom names and all coordinates at the start of your run.

I also think you should be able to use arbitrary files as long as the 
number of
atoms in the groups you compare are identical, but there might be 
problems if
you e.g. added hydrogens or created dummies  while the reference PDB 
doesn't have these...

Cheers,

Erik