Woah - as Carlos pointed out, you're creating a histogram with maybe
as many as 144 dimensions (one for each phi and psi)! That's certainly
not easy to visualize.
If instead what you wanted was to create a 2d histogram for each
phi/psi pair you can use a loop, e.g.
multidihedral DIH phi psi resrange 1-72 out PhiPsi.dat
for RES=1;RES<=72;RES++
hist DIH[phi]:$RES DIH[psi]:$RES min -180 max 180 bins 100 free 300
out test.$RES.gnu
done
Caveat: I haven't tested the above input but I think it should work.
See the manual for full details on using 'for' loops in cpptraj.
-Dan
On Wed, Aug 24, 2022 at 10:06 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Aug 24 2022 - 08:00:10 PDT
