Dear Amber users,
I'm trying to simulate a peptide which has a synthetic linker connecting
the C-terminal ends to two polypeptide chains. The structure looks like
this:
N-chain1-C-linker-C-chain2-N
I have gone through the tutorial B5 Simulating the Green Fluorescent Protein
<
http://ambermd.org/tutorials/basic/tutorial5/> and I understand how to
create a custom residue; if this was a synthetic linker between C and N,
the linker could be modelled as a "residue" and I'd be all set, but in this
case it's hard to see how to do that and also reverse the chain direction.
Is there some way to create a system of the type I'm trying to model?
More broadly, is there a general way to model covalent linkages between
multiple protein chains, including a linker? (anything including
sidechain-sidechain, head-tail, tail-tail, head-head, sidechain-tail etc,
and including having a custom linker in between using GAFF)
Sincerely,
Alex
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Received on Sat Nov 21 2020 - 22:00:02 PST
