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
>this:
>
>N-chain1-C-linker-C-chain2-N
I think in this case, you need to create a PDB file looks like this:
...first protein, N->C
TER
...linker
TER
...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
