This functionality is not yet available but we will implement it in the next major Marvin release (5.3).
However, it is possible even now, with Marvin 5.2, after a conversion with molconvert which fuses the fragments into one molecule. Example:
molconvert sdf e.sdf -R frags.sdf -o unionFrags.sdf
unionFrags.sdf will contain the fragments in frags.sdf in a single molecule. Unfortunately currently you have to specify an empty molecule (e.sdf) to fuse the fragments to, but this difficulty will be eliminated in Marvin 5.3. From Marvin 5.3, the above will be available in this simpler form:
molconvert sdf frags.sdf -U -o unionFrags.sdf
If you have a file with R-group definition members with attachment points already set, then it is possible to fuse them as R-group definition members to a scaffold. Example:
molconvert sdf scaffold.sdf -R1 frags.sdf -o rmol.sdf
In both cases it is possible to specify a range of molecule indexes. In case of the R-group definition members, you can filter the input by accepting only 1 or only 2 attachment molecules. Refer to the MolConverter guide for details.