AMBER Archive (2006)

Subject: Re: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Sep 13 2006 - 12:59:10 CDT

'impose' command of Leap will change the bond/angle/dihedral angles. Check
out the manual. If your structure is a helical structure, though, impose
command will not work. I had such an experience; needed to creat 360
structures by changing one particular dihedral angle by 1 degrees each
time, but because the structure was helical, it didnt work. I solved
it at the end. Your case is linear, so should not be a problem.

Best,

On Wed, 13 Sep 2006, priya priya wrote:

> Dear
>
> I have loaded a linear sequence of 15 residue peptide....now i want to change the dihedral angles and want to start with the different conformation.
> Please suggest me the path for that.
>
> With Regards
> Priya
>
>
> ---------------------------------
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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