Merge pull request #2727 from peastman/excludewith

Fixed an error using virtual sites with patches

Merge pull request #2727 from peastman/excludewith
Fixed an error using virtual sites with patches
12f17a6c · peastman · GitHub · bdd1f78a · 23ff308e · 12f17a6c
Unverified Commit 12f17a6c authored Jun 03, 2020 by peastman Committed by GitHub Jun 03, 2020
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wrappers/python/simtk/openmm/app/forcefield.py wrappers/python/simtk/openmm/app/forcefield.py +1 -0

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--- a/wrappers/python/simtk/openmm/app/forcefield.py
+++ b/wrappers/python/simtk/openmm/app/forcefield.py
@@ -813,6 +813,7 @@ class ForceField(object):
                    newSite = deepcopy(site)
                    newSite.index = indexMap[site.index]
                    newSite.atoms = [indexMap[i] for i in site.atoms]
+                    newSite.excludeWith = indexMap[site.excludeWith]
                    newTemplate.virtualSites = [site for site in newTemplate.virtualSites if site.index != newSite.index]
                    newTemplate.virtualSites.append(newSite)
            return newTemplates