AMBER Archive (2008)

Subject: Re: AMBER: nmode analysis

From: Joachim Reichelt (Joachim.Reichelt_at_helmholtz-hzi.de)
Date: Mon Jun 30 2008 - 07:36:32 CDT

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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