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

[Anthony Cruz Balberdi]

On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham <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

>
> Mark
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