On Mon, Sep 20, 2004 at 11:36:03AM -0400, John Penniston wrote: > I ran the same model under both 6v2 and 7v7; it ran OK under 6v2, but > crashed under 7v7. The source file was an NMR structure (1MO8) of a protein > with bound ATP. Not long before the program crashed, it gave the following > warning message under 7v7 which had not appeared under 6v2:
It is impossible to diagnose your problem without seeing your input files. Tar them up, and send them to modeller-care@salilab.org.
Ben Webb, Modeller Caretaker
On Mon, Sep 20, 2004 at 11:36:03AM -0400, John Penniston wrote: > I ran the same model under both 6v2 and 7v7; it ran OK under 6v2, but > crashed under 7v7. The source file was an NMR structure (1MO8) of a protein > with bound ATP. Not long before the program crashed, it gave the following > warning message under 7v7 which had not appeared under 6v2:
This particular modeling case includes an ATP residue, and you need to be rather careful to match your topology file to your templates when dealing with non-standard residues. In this case, Modeller has constructed ATP with hydrogens, as the 7v7 top_heav.lib topology includes hydrogen atoms for non-standard residues. 6v2's top_heav did not. Because the template does not include hydrogen atoms, Modeller is confused when it tries to add restraints.
Suggested solutions: 1. Edit top_heav.lib, and delete the hydrogens from ATP. 2. Use the ATP residue from 6v2's top_heav.lib.
Ben Webb, Modeller Caretaker
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John Penniston -
Modeller Caretaker