AMBER Archive (2009)

Subject: Re: [AMBER] nmoldyn2 with Amber

From: David Watson (dewatson_at_olemiss.edu)
Date: Sun Mar 08 2009 - 09:54:57 CDT

On Mar 8, 2009, at 9:37 AM, Adrien Delmont wrote:

> Dear All,
>
> I want to use nmoldyn2 with Amber 10 trajectory files for analysis.
> But I think I should need a Amber trajectory file converter for
> nmoldyn2 according to the User’s Guide. But I coudn't find the
> converter. Could you please give me the information where I can get
> the converter ? I'm waiting for your help.

It appears (cf. http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/nmoldyn-2)
  that nMOLDYN 2 uses netCDF format for the trajectory output, so you
should not have to convert the trajectory file at all if you are using
ioutfm=1 in your amber input files. If you already have a file in
amber coordinate format, then just use ptraj to read in your
trajectory and then output netCDF from ptraj.

>
> Thanks in advance
>
> Adrien
>
>
>
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