On 5/28/10 6:31 AM, Renuka Robert wrote: > I want to model ONLY magnesium ion (from protein B) on an already > crystallized structure (protein A). So the sequence of my target and > template is exactly the same. My alignment file is
Can you send me (not the list) your structure files too, please? I can't reproduce your problem (and thus fix the bug) without them. It is definitely a Modeller bug though (not something wrong with your inputs): Modeller should never crash with a segfault, regardless of what you feed it.
I think the surface area calculation is getting confused since you have no amino acid resides in one structure (but I'll need to check with your inputs). As a workaround, you can use the BLK residue '.' rather than '$'. Since MG is just a point anyway, your modeling results should be almost identical.
Ben Webb, Modeller Caretaker