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Re: [modeller_usage] Including a Thioester linkage

João Rodrigues wrote:
Another question though, maybe this is a bit out of the scope of MODELLER but:

PRES DISU         -0.36 ! Patch for disulfides. Patch must be 1-CYS and 2-CYS.

ATOM 1:CB  CT2    -0.10 !
ATOM 1:SG  SM     -0.08 !           2:SG--2:CB--
ATOM 2:SG  SM     -0.08 !          /
ATOM 2:CB  CT2    -0.10 ! -1:CB--1:SG

So, I get the syntax but I fail to understand one thing. Is that number -0.36 the overall charge of the residue or something?

Yes, that's the total charge. Modeller doesn't actually depend on this being correct, however, so you can set it to 0 if you like. You can't leave it blank though.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage