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Re: [modeller_usage] Including a Thioester linkage

João Rodrigues wrote:
So, I've managed to build the topology:

Everything looks OK to me, although you might want some IC (internal coordinate) entries in there too to get the initial conformation correct if you're going to build extended chains using this topology.

In the visualisation program that is. In the PDB file, it all seems ok actually, but for the two lines next to the bond:

ATOM 7740 OE1 GLN B 984 -52.638 -33.311 -71.659 1.00326.32 O ATOM 7741 C GLN B 984 -51.735 -35.089 -72.840 1.00 0.00 C ATOM 7742 O GLN B 984 -51.735 -35.089 -72.840 1.00 0.00 O ATOM 7743 N ASN B 985 -50.555 -32.594 -69.198 1.00326.32 N

I don't how that it would happen that two atoms would end up superposed like that, since you haven't changed the bonds within the GLN.

	Ben Webb, Modeller Caretaker
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