AMBER Archive (2007)

Subject: Re: AMBER: vmd and amber

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Tue Apr 17 2007 - 07:33:48 CDT

You have at least 2 options there:

1. If you just want to see a plot, you can use VMD's ramaplot tool:
    Extensions => Analysis => Ramachadran Plot.
    There you can also generate a 3D histogram of the phi/psi map, but I
was never able to save the data.

2. If you want the data, then you can use ptraj to generate files with
the angles you need. For example, for alanine dipeptide, we could use:

    trajin ala-di.crd
    dihedral phi :1_at_C :2_at_N :2_at_CA :2_at_C out PHI.DAT
    dihedral psi :2_at_N :2_at_CA :2_at_C :3_at_N out PSI.DAT

    The atom definitions here should give you the phi/psi angles for
alanine dipeptide.

HTH,

Gustavo.

deepti nayar wrote:
> hi all
>
> I am doing something similar to the NEB tutorial by Ross Walker. at
> the end of the simulation a large number of conformations are
> generated. i visualize all trajectories in VMD together in all frames.
> whrn i have to calculate the psi and phi angles, i select the 4 atoms
> once and thn keep changing tframes and automatically psi and psi value
> keep changing for each one of them.
>
> bt since large no of conformers are generated, is thr any way out that
> the angles are listed so that a graph can be easily mapped?
>
> please guide me.
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