Re: [modeller_usage] Crash under 7v7

[Modeller Caretaker <modeller-care@ucsf.edu>]

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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