I am not quite sure what your problem is, but it seems that you find that the protein is not completely within the box. You have decided to use the box dimensions given in the usage example in solvent-box.str, and this may not be appropriate for crambin. You have to change the dimensions to suite your problem. Note that a rhombic dodecahdron (RHDO), which is symmetric, may be a better shape than a cube or a prism since its volume is smaller for a given distance between the primary solute and its images. There are examples of how to setup the RHDO in the Script Archive.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden