[AMBER] Tail-to-tail peptide linker?

From: Alexander Izvorski <aizvorski.gmail.com>
Date: Sat, 21 Nov 2020 21:53:50 -0800

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


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)

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Received on Sat Nov 21 2020 - 22:00:02 PST
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