[gmx-users] tpbconv and tpr file problem...

Mark Abraham Mark.Abraham at anu.edu.au
Fri Mar 16 15:37:21 CET 2012

On 17/03/2012 12:39 AM, Anthony Cruz Balberdi wrote:
> On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote:
>         Hi Users:
>         I was trying to calculate the energy contribution of an
>         specific ion in my simulation. After extract a given frame
>         from the simulation, I recalculate the energies of this frame
>         with mdrun -rerun. Then I used tpbconv and editconf to create
>         a new gro file and a new tpr without the ion. I tried to run
>         mdrun -rerun with this new files but the mdrun stops with the
>         following error:
>         Program mdrun, VERSION 4.5.5
>         Source code file: domdec_top.c, line: 744
>         Software inconsistency error:
>         Not enough position restraint coordinates
>         What could be the problem?
>     Probably some [moleculetype] now has insufficient atoms to cope
>     with its position restraints, which apparently weren't edited
>     (correctly) by the tpbconv subset procedure.
>         Any possible solution?
>     Probably depends on your use of position restraints, which would
>     have been a good thing to have included in your original post....
> Thank for your answer and sorry for the missing information. The 
> position restraint is acting on the protein backbone. Since has 
> nothing to do with the ion, I dont understand why the error...
> Anthony

OK, so maybe tpbconv subsets don't work well with position restraints. 
You can probably do what you want with a suitable combination of energy 
groups and mdrun -rerun.

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