AMBER Archive (2007)

Subject: Re: AMBER: side chain orientation

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Feb 07 2007 - 12:00:37 CST

Dear Esther,

I did not understand exactly what you want to do. Do you want to calculate
the dihedral angles of some part of your structure or do you want to
visualize it? VMD will be useful to visualize these structures. If you
have 2 structures, you can use the RMSD Calculator in VMD to align these 2
structure.

What I did not understand is, do u have 2 structures, or 1 structure? If
you have 2, VMD will help u to align and visualize them. If there is 1
structure, I am not clear what u want to do; calculate the backbone
dihedral angles of that particular aminoacid residues? You can do this
with ptraj. You need to write a script, which will do everything
automatically, or if there arent that many dihedral angles there, u can do
it manually, too.

Best,

On Wed, 7 Feb 2007, Esther Brugger wrote:

> Dear Fenghui,
>
> Thanks for your reply.
>
> In my calculation, there are 2 amino acids in different side of the backbone. Now I am trying to use some figures to show these 2 amino acids in the different direction becasue of the steric hinder effect. For example, if there is no steric hinder effect, they are probably in right side of the bacbone; but now one is in the left side, the other is in the right side. I tried dihedral angle and angle to get it by ptraj program through trajectory file, but the results didn't show what I want. I really wish you may help me figure it out. Thank you very much for your time and help!
> Bests,
>
> Fenghui Fan <fenghui_fan_at_yahoo.com> wrote: As for a protein, it should has it PDB file. Then the
> coodinates of the two side chains has been decided,
> then you can know the orientation. I do not know
> whether this is what you want. If not, please tell me
> a little in detail on what you really want to get.
>
> Best regards.
>
> Fenghuin Fan
>
>
> --- Esther Brugger wrote:
>
> > Dear Amber Users,
> >
> > Does anyone know which program can be used to
> > calculate the orientations of two amino acids which
> > are in the different side of backbone of the
> > molecule?
> > Any advice are appreciated!
> > Bests,
> >
> >
> >
> > Esther B.
> >
> >
> > ---------------------------------
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>
> Esther B.
>
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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