Re: [modeller_usage] Including a Thioester linkage

[Modeller Caretaker <modeller-care@salilab.org>]

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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