Amber does not provide any zwitterionic amino acid residues by default.
You can find some here: http://www.pharmacy.manchester.ac.uk/bryce/amber/
Besides that, you will actually have to tell us what you tried (i.e., are
these residues part of a PDB file? Are you using the "sequence" command?
"combine"?). But if you want to use zwitterionic residues, you need to
download the database from the website above and make sure the residue name
of the amino acid "ligand" matches the residue name inside the zwitterion
library.
HTH,
Jason
On Sat, Apr 11, 2015 at 11:06 PM, Dhiraj Srivastava <dhirajks.gmail.com>
wrote:
> How can I include amino acid as ligand and not as residues in xleap? My
> protein binds to amino acid and xleap is treating it as residue removing
> one of the oxygen from carboxylate group.
> thanks
> Dhiraj
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Apr 11 2015 - 21:30:02 PDT
