Frequently Asked Questions

This section compiles some of the most often encountered issues running an AdaptivePELE simulation.

  • Not having AdaptivePELE in your PYTHONPATH variable. If you get an error like:

    ImportError: No module named AdaptivePELE

    python is not able to find the adaptive module. You need to add the path as:

    export PYTHONPATH="/path/to/repo/AdaptivePELE:PYTHONPATH"

  • Similar to the previous message, if the module affected is one of atomset, freeEnergies.utils, RMSDCalculator or SymmetryContactMapEvaluator, the issue might be that the cython extension of AdaptivePELE are not compiled, to do so find the setup.py script in the AdaptivePELE repository and run:

    python setup.py build_ext --inplace

  • Simulation dies with no error. This happen sometimes in a PELE simulation, almost always is related to a PELE error that was not handled properly. One frequent source of this issue in simulation running in the life or nord clusters is a bug of mpi that requieres to declare the following environment variables:

    export OMPI_MCA_coll_hcoll_enable=0
export OMPI_MCA_mtl=^mxm

  • If you get an error including the message:

    No trajectories to cluster! Matching path:

    adaptivePELE has not been able to find trajectories to cluster. This is tipically because the simulation died before it could produce any trajectories, in such case check for PELE errors.

  • If you get an error like:

    UnsatisfiedDependencyException: Missing package....

    it means that an optional dependence is missing. That is a package that is not absolutely required to run AdaptivePELE but it is needed for some particular feature that you are using cannot be found. To solve it ensure that the package in question is installed and accessible to the python interpreter (e.g check the PYTHONPATH value)

  • There is a weird atom named DUM in my trajectories! When using MD with an spherical box for the ligand, a dummy atom is introduced to act as the center of the box and is listed in the trajectories as DUM atom in a residue also named DUM. This atom is massless so it will not be moved during the simulation.

  • Ligand preparation for MD fails with a ligand containing a Cl atom. With a tleap error like:: FATAL: Atom .R<SCH 218>.A<Cl1 22> does not have a type.

    check that the ligand’s Cl atom in named “Cl” and not “CL”, so that antechamber recognizes it properly. This might happen with other atoms, if so we will update this site with their examples.