> On Feb 1, 2015, at 12:36 AM, Robert Molt <rwmolt07.gmail.com> wrote:
>
> I do beg pardon if this answer is obvious; I could not discern this from
> the AmberTools manual.
>
> Is it possible, in using the xleap interface, to construct a sequence
> composed of a single amino acid in zwitterion form? It's clear how to
> make zwitterions for two or more amino acids, but I have an unusual
> purpose for which I need a single amino acid zwitterion..
>
> If this is not an option, can one advise how one might construct a
> zwitterion form in an easily recognizable for the prmtop file?
Amber does not have any zwitterionic residue definitions in the available library files -- you will need to create your own residue library (e.g., using antechamber) to derive the charges and connectivity. It’s really no different than parametrizing an arbitrary organic ligand.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Feb 01 2015 - 05:00:02 PST
