AMBER Archive (2008)

Subject: Re: AMBER: Ring flips

From: David Watson (dewatson_at_olemiss.edu)
Date: Fri Oct 10 2008 - 12:30:37 CDT

On Oct 10, 2008, at 12:09 PM, Beale, John wrote:

> I would like to determine if and how often phenylalanine and
> tyrosine undergo ring flips during a protein MD. Can someone
> recommend to me a way that I can do this?
>
> John
>

I suppose you could monitor it with a trajectory file:
trajin my_md_coord_file
dihedral my_variable_name :1_at_CD1 :1_at_CG :1_at_CB :1_at_CA out
my_results_file_name

1) make sure you select the correct residue number (don't use "1"
unless that's what you want to do.

Then after running it through ptraj, inspect the number of times the
sign changes direction.
That's about all I can suggest, but there are some problems with this...

2) The dihedral may change sign without necessarily following a full
360 degree flip and
3) depending upon the frequency with which you output MD coordinates,
you may altogether miss sign changes
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