AMBER Archive (2008)

Subject: RE: AMBER: nmode analysis

From: Vahdati N. (nadiav_at_soton.ac.uk)
Date: Mon Jun 30 2008 - 07:41:40 CDT

Hi,
Just put a .pev extension on the eigenvector file you obtained from nmode and you can read this into IED. You load a pdb and then this .pev file.
Have a look at this communication on amber archive:
http://structbio.vanderbilt.edu/archives/amber-archive/2004/1805.php
Regards,
Nadia
________________________________________
From: owner-amber_at_scripps.edu [owner-amber_at_scripps.edu] On Behalf Of Joachim Reichelt [Joachim.Reichelt_at_helmholtz-hzi.de]
Sent: 30 June 2008 13:36
To: amber_at_scripps.edu
Subject: Re: AMBER: nmode analysis

As far as I can see IED uses the output from ptraj/rdparm
Both are not reading the vecs file nmode writes out.
So you have to run e.g. sander to get a tarjectory.
So what are these vecs good for?

Mark Williamson schrieb:
> Joachim Reichelt wrote:
>
>> So what program can be used to visualize the modes. VMD does not uses
>> them but the tarjectories.
>
> You might want to try Interactive Essential Dynamics, since IIRC this
> can do what you want:
>
> http://mccammon.ucsd.edu/ied/
>
> http://dx.doi.org/10.1007/s10822-004-4121-z
>
>
> regards,
>
> Mark
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--
Joachim
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