Thanks for the help Jason! I will check out OpenMM for this!
Best!
Morgan
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Monday, December 15, 2014 2:42 PM
To: AMBER Mailing List
Subject: Re: [AMBER] gas phase, nonperiodic system with AMOEBA ff in AMBER
Hi Morgan,
On Mon, Dec 15, 2014 at 3:17 PM, Lawrenz, Morgan <mlawrenz.amgen.com> wrote:
>
> Hi all,
> I want to perform a gas-phase protein simulation (to compare with gas
> phase structural biology experiments) using the AMOEBA ff.
>
Then
I'm afraid you'll have to use another software. The alternative is to introduce a large periodic box with no solvent, but then you will still have the periodic images of the solute interacting with each other.
But I only think PME is supported for the multipole force in the Amoeba force field (someone will hopefully correct me if I'm wrong). Alternative softwares capable of this calculation include Tinker and OpenMM, if I'm not mistaken (the latter of which you've probably had perhaps a passing acquaintance with ;).
Good luck, and I hope all is going well, Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 15 2014 - 15:00:03 PST
