Re: [AMBER] residue wise rmsd, not getting expected results

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Mon, 12 Jul 2010 09:41:29 -0700

> Please suggest what changes I should make to the input so as to plot
> fluctuations in the backbone of the H-12 helix (residue 259-271). How can I
> get residue wise rmsd on the y-axis and residue no. on x-axis in the plot?
> This way I will be able to show that backbone rmsd for selected residues is
> more in some cases and less in other.

I suspect you will have to manually patch together your plot
from ptraj output. Hopefully there is a way to specify per-
residue rms without a fit. This would give a time series of
rms per residue, but what you want might be the average over
time for each residue. If ptraj doesn't calc this, you might
need to do it manually. Then you could make your plot file:

<res_num> <avg_rms>

I haven't used ptraj but you could read the manual to see
how to get per-residue rms and what the output format is.


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Received on Mon Jul 12 2010 - 10:00:03 PDT
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