VMD-L Mailing List
From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Thu Feb 04 2016 - 10:10:25 CST
The divide-and-conquer strategy is very much applicable to ffTK, which is designed to follow the principles underlying the CGenFF (and CHARMM) force fields. If you already have charges (by analogy or some other method), you can skip the ChargeOpt step; however, you will still need to perform the GeomOpt step in oder to compute a low energy conformation as a consistent reference frame that is utilized by multiple subsequent steps. Also, the checkpoint files that are output during the initial geometry optimization are required input for the Calc Bonded step.
> On Feb 4, 2016, at 3:37 AM, fvlieffe <Francois.Van.Liefferinge_at_ulb.ac.be> wrote:
> Hi all,
> I fully parametrize with success 2 molecules with fftk. I did that in order to get parameters for a bigger molecule
> including the 2 previous one following the "divide-and-conquer" strategy.
> This strategy is explain quite well by the CGENFF method developpers (the Mackerell team).
> Is it also applicable for fftk?
> The charges can be developped by analogy with the CGENFF method so I guess for the full molecule
> I should start with the "calc bonded" step?
> thank you for your answer
> Van Liefferinge François
> Phd Student in Chemistry
> S.F.M.B., Université Libre de Bruxelles
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