AMBER Archive (2006)

Subject: Re: AMBER: post nmanal

From: $B?y?9_at_5F;(B
Date: Mon Sep 11 2006 - 01:09:28 CDT

Thank you for quickly responding.
I would like to know especially how to make ptraj read vec file made
by nmode to analyze it.
If possible, I would like to culculate the rms fluctuation of small
protein by residue as I have analyzed MD trajectory by command of
"atomicfluct out filename @CA,C,N byres".

Best regards,

2006/9/10, David A. Case <case_at_scripps.edu>:
> On Sat, Sep 09, 2006, ?$B?y?9_at_5F; wrote:
> >
> > I would like to do post processing of vector made by nmode, but nmanal
> > is no longer available. Can anyone tell me the method of the post
> > processing by ptraj?
>
> What sort of analysis do you want to do? That is, what properties are you
> trying to compute?
>
> The basic ptraj commands are "analyze modes", "analyze matrix" and "projection
> es". These are all described in the Users' Manual (pp. 259-260 for Amber9).
>
> ...dac
>
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