yes I suggest ff99SB.
On Tue, Mar 30, 2010 at 6:26 AM, Mannan <malie_03.yahoo.co.in> wrote:
> Thanks for the comments.
>
> Still would you suggest any specific force field for peptide simulations?
>
> Mannan.
>
>
>
> --- On Mon, 29/3/10, Carlos Simmerling <carlos.simmerling.gmail.com>
> wrote:
>
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Subject: Re: [AMBER] AMBER ff99sb
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Monday, 29 March, 2010, 5:02 PM
>
> what you probably heard is that the backbone parameters are better in
> ff99SB, but that Ile can be improved in all amber force fields including
> 99SB. ff94 performs worse than 99SB, but in very short (ns) runs you are
> probably OK.
>
>
> On Mon, Mar 29, 2010 at 5:04 AM, Mannan <malie_03.yahoo.co.in> wrote:
>
> >
> > Dear Amber users,
> > I was recently told that the dihedral parameters for amino acid
> > Isoleucine is incorrect except in ff99sb. I used ff94 for my peptide
> > simulations with Ile. Wonder which force field is good for peptide
> > simulations of 13mer?
> > I used ff94, since it matched well for few experimentally observed
> trends.
> >
> > Thanks for any suggestions and comments
> >
> > Mannan
> >
> >
> >
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Received on Tue Mar 30 2010 - 04:30:04 PDT
