Dear all,
I found out that changing the data format from .agr to .dat gave me exactly what I wanted. Therefore the solution is:
parm native_hex.prmtop
trajin productions/prod_1.nc
multidihedral d phi psi chip out test.agr
go
avg d[*] out avg.dat name angles
Best
Martin
> On 13. Oct 2022, at 16:33, Rosellen, Martin via AMBER <amber.ambermd.org> wrote:
>
> ⚠ Caution: External sender
>
>
> Dear Amber mailing list,
>
> I wanted to calculate averages of dihedral angles of a whole hexamer with the following lines:
>
> parm native_hex.prmtop
> trajin productions/prod_1.nc
> multidihedral d phi psi chip out test.agr
> go
> avg d[*] out avgi.agr name angles
>
> I learned, that ‘avg' produces a line number with the calculated average for every dataset (one for each residue and angle) found in d[*]. For a structure of 50 residues, line numbers would go up to 150 therefore and it would be possible to map line numbers back to residue numbers. To make it even easier, I ran the following lines:
>
> parm native_hex.prmtop
> trajin productions/prod_1.nc
> multidihedral d phi psi chip out test.agr
> go
> avg d[psi] out avg_psi.agr name psi
> avg d[phi] out avg_phi.agr name phi
> avg d[chip] out avg_chip.agr name chip
>
> For psi and phi angles, the output files look fine. An issue remains with avg_chip.agr. Since a chi1 angle can’t be calculated for all residues (e.g. ALA, GLY) the line numbers can’t be easily mapped back to residue numbers.
>
> The idea that I would try next is:
>
> parm native_hex.prmtop
> trajin productions/prod_1.nc
> multidihedral d phi psi chip out test.agr
> go
> avg d[psi]:1 out avg_psi.agr name psi_1
> avg d[phi]:1 out avg_phi.agr name phi_1
> avg d[chip]:1 out avg_chip.agr name chip_1
> avg d[psi]:2 out avg_psi.agr name psi_2
> avg d[phi]:2 out avg_phi.agr name phi_2
> avg d[chip]:2 out avg_chip.agr name chip_2
> …
> avg d[psi]:1332 out avg_psi.agr name psi_1332
> avg d[phi]:1332 out avg_phi.agr name phi_1332
> avg d[chip]:1332 out avg_chip.agr name chip_1332
>
> Is there maybe an easy way to get residue numbers into the avg output file next to calculated values?
>
> cheers
> Martin
>
>
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Received on Fri Oct 14 2022 - 07:30:02 PDT
