Re: [AMBER] Tail-to-tail peptide linker?

From: David A Case <>
Date: Sun, 22 Nov 2020 08:57:30 -0500

On Sat, Nov 21, 2020, Alexander Izvorski wrote:
>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 think in this case, you need to create a PDB file looks like this:

...first protein, N->C
...second protein, N->C

after loadPdb, use the bond command to create the cross-links you want
between the linker and the two protein chains.

The downside of this is that the residue numbering for the second
protein will still be in the N->C direction. I can't immediately think
of any easy way around this. (A number of subtle parts of both setup
and analysis assume that proteins are described N->C; it's probably
easier to live with it than to try to change it.)

As always, maybe someone on the list has a better idea.

...good luck....dac

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Received on Sun Nov 22 2020 - 06:00:03 PST
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