On Thu, Mar 09, 2017, Michael Shokhen wrote:
>
> I have on my Linux server Amber16 and AmberTool16.
> I need to simulate by MD enzyme with deprotonated side
> residue oxygen atom (anionic OG atom) of catalytic Ser.
> The ff14SB force field used for the simulation
> has no parameters for such a case.
> What is the best way to resolve the problem?
The R.E.D. server might already have this residue, and in any event offers
a nice environment for generating force fields for modified residues.
A second alternative is to follow tutorial B5 to generate your modified amino
acid. Nothing is really easy, however, since the Lennard-Jones parameters
needed for a deprotonated hydroxyl oxygen might need to be tuned via quantum
calculations.
....dac
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Received on Thu Mar 09 2017 - 06:30:04 PST
