On Thu, Jun 24, 2010, Catein Catherine wrote:
>
> Can I used DA instead of DA3 or DA5 for the terminal residues?
Yes, but you need to edit your leaprc file. Most of them (e.g. ff99bsc0)
have an addPdbResMap section which automatically converts a terminal
DA residue into DA3 or DA5. If you remove that mapping, then you can have
DA as a terminal residue. You will have a dangling bond in that residue,
however, since DA is designed to be in the center of a strand. You probably
really want to copy DA to some new residue name, and modify that to have
exactly what you want at the end of your strands. Amber doesn't really make
it all that easy to do this....
....good luck...dac
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Received on Thu Jun 24 2010 - 08:00:04 PDT
