AMBER Archive (2008)

Subject: Re: AMBER: Inquiry on analyzing the amplitude from nmdout results

From: James Thomas (james.protein_at_googlemail.com)
Date: Wed Mar 19 2008 - 17:00:35 CDT

Dear Prof. Case

Thanks a lot for the answer. Yes, I have set nvect > 0. Is there an online
tutorial on how to interpret the "vecs" file results? I could not find about
this from amber9 manual.
Can I use the ptraj commands to analyze them?
Thank you very much!

On Wed, Mar 19, 2008 at 9:46 PM, David A. Case <case_at_scripps.edu> wrote:

> On Wed, Mar 19, 2008, James Thomas wrote:
> >
> > I just finished run the nmode program, using the ntrun=1, after doing
> > minimization with ntrun=4. However, the results has not information on
> > amplitude, is there any other setting that I should set before that?
> > I only obtained energy & entropy information, but not the amplitude that
> I
> > want.
>
> The eigenvectors are written to the "vecs" file, provided you have set
> nvect
> to a value greater than 0.
>
> ...dac
>
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