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martimunicoy / peleffy

The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.

Home Page:https://martimunicoy.github.io/peleffy

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Invalid atom ordering in Impact template

martimunicoy opened this issue · comments

commented

Description

We detected extremely large computational times in the Side Chain Prediction algorithm when using Impact templates generated with peleffy. The reason of this undesired behaviour seems to be a consequence of a bad atom ordering in these templates. Atoms are not properly sorted by their parent indices.

Solution

Fix the ordering in the Impact template.

commented

Extended description

Now we know that the atoms in the Impact template need to be sorted by two criteria:

  • Atom location: first atoms from the core, then atoms from the side chain
  • Parent index: ascending order of parent indices according to the molecular graph

The problem was that, although atoms where correctly sorted by atom location, they were not following the right criteria with parent indices. As a result, PELE was able to load molecular topologies with no problem but, in some cases, this bad ordering lead to problems when running the side chain prediction algorithm. In these cases, side chain prediction algorithm could require a large computational time (e.g more than 1000s).

This issue seems fixed with the correct order of the atoms in the Impact template file.