[gmx-users] tpbconv and tpr file problem...
Anthony Cruz Balberdi
anthony.cruz5 at upr.edu
Fri Mar 16 15:46:47 CET 2012
On Fri, Mar 16, 2012 at 10:37 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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>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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