Currently the Sire::IO::AmberPrm parser doesn't respect the NUMEXTRA AMBER flag, which means that we can't run simulations with TIP4/5p water models in BioSimSpace. See here and here for discussions of the issue.
Hopefully this is an easy fix, i.e. counting the number of dummy atoms in the system and adding the appropriate NUMEXTRA flag on write. (It is currently always set to zero.) We don't need to worry about reading the flag, since we don't use it internally, and can always reconstruct it by counting dummies.
Currently the
Sire::IO::AmberPrmparser doesn't respect theNUMEXTRAAMBER flag, which means that we can't run simulations with TIP4/5p water models in BioSimSpace. See here and here for discussions of the issue.Hopefully this is an easy fix, i.e. counting the number of dummy atoms in the system and adding the appropriate
NUMEXTRAflag on write. (It is currently always set to zero.) We don't need to worry about reading the flag, since we don't use it internally, and can always reconstruct it by counting dummies.