The old-style motif virtual was removed, see bug 224749 and my announcement in gentoo-dev four weeks ago. Dependency should be changed from virtual/motif to x11-libs/openmotif for the following ebuilds in the Science Overlay: sci-biology/cluster-1.38 sci-chemistry/gromacs-3.3.3 sci-misc/praat-5.0.01
Thanks for the heads up!