[BUG] sire.morph.create_from_pertfile doesn't assign different element properties to the end states
lohedges opened this issue · 0 comments
Not really a bug, since this works for the purposes of running simulations with somd2
, which is the intended use case, but the sire.morph.create_from_pertfile
function doesn't assign different elements to the end states when atoms are perturbed. (The element0
and element1
properties are identical.) This is because element
is absent from the perturbation template and atom changes are inferred from the ambertype0
and ambertype1
properties.
This is currently causing round-trip pert file conversion to fail, since the file written back by BioSimSpace differs since it uses the element property to check for dummies, which will be wrong if there is a dummy in the lambda = 1 state. A minimal fix would be to set the appropriate end state property to Element(0)
if either ambertype0
or ambertype1
is du
. A full fix would be to correctly set the lamba = 1 element property for all atoms, potentially inferring from ambertype1
.