I haven't done exactly this, but I would probably try to split the new
residue into halves and insert them as a modified nucleotide and modified
amino acid, and then use the bond command to connect them. the parameters
will all work out fine no matter which way you break it up for the
"residue" definitions. then you still have continuous DNA and protein
chains, too.
On Fri, Oct 9, 2015 at 12:35 PM, Jackle, Chasen <chasen.jackle.uleth.ca>
wrote:
> Hi Amber experts,
> So we have a non-standard residue which is a Schiff base in a DNA-protein
> complex, we've parameterized the residue (an amino acid linked to a
> ring-opened deoxyribose). The problem is how to assign this residue to the
> chain(s). Protein is chain A and DNA is chain B, if we assign the Schiff
> base to DNA, there will be a break in the protein chain and the same thing
> happens to the DNA if we assign the linkage to the protein. Changing the
> name of chains (both DNA and protein) to one chain (A for example) didn't
> work either.
> Any suggestion/help is highly appreciated.
> Thanks in advance,
> Chasen
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Received on Fri Oct 09 2015 - 10:00:04 PDT
