parmbsc0 is the only ff Cornell et al variant that gives stable DNA
trajectories, so, it is essential for DNA.
It combines well with ff99SB for the protein part.
Jiri
On Mon, 4 Feb 2013, Sangita Kachhap wrote:
> Date: Mon, 4 Feb 2013 18:09:14 +0530 (IST)
> From: Sangita Kachhap <sangita.imtech.res.in>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: amber.ambermd.org
> Subject: [AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB
>
> Hello All,
> I have a small query regadring force field. parmbsc0 is modified force filed of
> ff99 for DNA and it is used with ff99SB for MD simulation of DNA.
> Since irreversible α/γ transitions from the canonical to a non-canonical
> sub-state, accompanied by severe distortions of the structure associated with
> ff99 thus to remove this it was modeify to parmbsc0.
>
> So I have one query should I use parmbsc0 along with ff99SB when doing MD
> simulation of protein-DNA complex?
>
>
> With regards
> Sangita Kachhap
> SRF
> BIC,IMTECH
> CHANDIGARH
>
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Received on Mon Feb 04 2013 - 05:30:03 PST
