This looks like you're trying to make a 72 dimensional data set? You'll
need to reduce that. There is a lot of literature and methods for
dimensionality reduction, but it really depends a lot on your goals. If
it's dynamics of the foded protein, maybe PCA is a good place to start.
On Wed, Aug 24, 2022, 9:06 AM ning via AMBER <amber.ambermd.org> wrote:
> Hi Amber experts,
>
>
> I want to convert a dihedral dataset of protein who have 72
> residues into a PMF plotting. I used this scripts as following:
>
> parm *.prmtop
>
> trajin *.nc
>
> multidihedral DIH phi psi resrange 1-72 out PhiPsi.dat
>
> hist DIH[*] min -180 max 180 bins 100 free 300 out test.gnu
>
>
>
>
> Whereas, my plotting looks like be completely wrong. Please help me, what
> is the wrong with this script? Thanks in advance.
>
>
>
>
>
>
>
> Sincerely,
>
> Ning
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Received on Wed Aug 24 2022 - 07:30:19 PDT
