This package uses variables banned in some scopes. This may stop working in future versions of Portage.
$ pkgcheck scan -k VariableScope sci-chemistry/vmd
VariableScope: version 1.9.4_alpha51: variable 'ED' used in 'src_prepare', lines 132, 133
VariableScope: version 1.9.4_alpha55: variable 'ED' used in 'src_prepare', lines 131, 132
I don't know how to apply PREFIX changes in other way... they need to be applied before configure is run :/