Re: [AMBER] normal mode analysis, AmberTools13, vecs

From: case <>
Date: Thu, 7 Nov 2013 07:54:20 -0500

On Thu, Nov 07, 2013, maghtar wrote:
> It seems nomde() has been under ptraj before but it is through NAB now. I
> am not sure if the ouputs are same.

I think you are confusing normal mode analysis with quasiharmonic analysis.
The former is done with NAB, the latter with ptraj (or now, with cpptraj).
I think the output formats for the vecs file are the same.

> So far I have only found this software:
> but I have difficulties to install it.

The IED plugin is now outdated, since the way VMD interacts with python has
changed. You might look here: (Note:
I've not used this one myself.)


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Received on Thu Nov 07 2013 - 05:00:03 PST
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