Thank you so much for clarifying.
On 3 November 2016 at 18:18, Jason Swails <jason.swails.gmail.com> wrote:
> Those force fields use a different functional form for the dihedrals
> (Ryckaerts-Bellemans) I believe, which is equivalent to what amber uses as
> long as the phase shifts are either 0 or 180 degrees.
>
> However, ParmEd does not yet have the ability to convert between the two
> functional forms. So even though it should be possible, I don't think it is
> yet.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
>
> > On Nov 2, 2016, at 10:05 PM, Dd H <ddhecnu.gmail.com> wrote:
> >
> > You mean I should upgrade to the newest version?
> >
> >> On 3 November 2016 at 09:58, Nhai <nhai.qn.gmail.com> wrote:
> >>
> >> The newest version in AT16 is 2.6.1
> >>
> >> Hai
> >>
> >>> On Nov 2, 2016, at 9:13 PM, Dd H <ddhecnu.gmail.com> wrote:
> >>>
> >>> I checked the version of parmed using this command: "parmed -v" and
> it's
> >>> version 2.0.5
> >>>
> >>>
> >>>>> On 3 November 2016 at 09:00, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >>>>>
> >>>>> On Wed, Nov 2, 2016 at 8:56 PM, Dd H <ddhecnu.gmail.com> wrote:
> >>>>>
> >>>>> Hi Jason,
> >>>>> The system contains a protein, a ligand, water and counter ions, and
> >>>>> AMBER99SB force field and GAFF are used. I think the input files are
> >>>>> ordinary. So I don't know why it failed.
> >>>>>
> >>>>
> >>>> which version you're using? you might want to upgrade to AmberTools16
> >>>>
> >>>> Hai
> >>>>
> >>>>
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Received on Thu Nov 03 2016 - 06:00:03 PDT
