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