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Re: [modeller_usage] Including a Thioester linkage

Thanks for the answers Ben, they have been quite useful. In fact, they always are. Congrats to you and the team for the efforts.

So, I've managed to build the topology:

PRES THIO          -0.18
ATOM 1:CB   CT2    -0.10
ATOM 1:SG   SM     -0.08
ATOM 2:CD   CC      0.55
ATOM 2:OE1  O      -0.55

This is based on the DISU Topology in the FAQ. Since the concept is pretty much the same, I thought both bonds would share the same characteristics. The thioester is just a sulphur attached to a carbon, with the deletion of a NH2 group from the Glutamine and a H group from the Cysteine (in my case).

I then set this like:

self.patch(residue_type='THIO', residues=(self.residues['981:B'], self.residues['984:B']))

And it apparently works. My structure does show a bonding of the two residues, albeit quite crooked when compared with the original. This is perhaps, the rest of the protein, from the bond onward just disappears. 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

This is the carbonyl group of the Glutamine residue involved in the thioester linkage. The last two factors are completely mismatching the surroundings and I think I might have made a mistake when building the topology. Maybe missing a BOND statement.

I'm trying to solve it on my own, but I have no experience either with this, or with CHARMM and so I might be heading down the wrong path. That's why I'm posting here. If you can give me a hint on what I'm doing wrong, or anyone else, I'd be thankful.

Best regards to all,

João [ .. ] Rodrigues

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