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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 15 01:42:37 CET 2012

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....


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