Some Amber files seem not to have box sizes (inpcrd) seem not to have box sizes. Parmed seems to create box sizes that are the minimal size to fit, but for small molecules, these boxes are far too small for reasonable cutoffs for energy evaluation.
Can be kluged around eventually, but probably there should be some checking of box size created by Parmed, and expanded if not big enough (size can be read from the cutoffs in default vacuum tests). Will have to think more about this.
Some Amber files seem not to have box sizes (inpcrd) seem not to have box sizes. Parmed seems to create box sizes that are the minimal size to fit, but for small molecules, these boxes are far too small for reasonable cutoffs for energy evaluation.
Can be kluged around eventually, but probably there should be some checking of box size created by Parmed, and expanded if not big enough (size can be read from the cutoffs in default vacuum tests). Will have to think more about this.