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 Thu Oct 13 2022 - 08:00:02 PDT
