AMBER Archive (2009)

Subject: Re: [AMBER] nmoldyn2 with Amber

From: David Watson (dewatson_at_olemiss.edu)
Date: Sun Mar 08 2009 - 15:00:39 CDT

On Mar 8, 2009, at 1:32 PM, M. L. Dodson wrote:

> On Sun, Mar 08, 2009 at 09:54:57AM -0500, David Watson wrote:
>> 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
>>>
>
> Actually, according to the nmoldyn-2 web site, it expects trajectories
> to be in MMTK format. CHARMM, X-PLOR, NAMD and DLPOLY are handled
> within the distribution, but a converter for AMBER trajectories is
> said to be available separately. However, when clicking the link it
> gave an Error 403, Access forbidden! message. It suggested to contact
> the webmaster, however the email address was given as root_at_localhost;
> not very helpful. I suspect just having an AMBER trajectory in netcdf
> format would not be sufficient, else why have a specific converter
> (and why handle the other MD programs individually?).
>
> Is there a general purpose AMBER to MMTK converter available?

As far as I can tell, page 13 of the NMOLDYN 2 User's Guide states
explicitly that input trajectories should be in netCDF format.
Perhaps the suggestion for a converter is due to the age of the web
page, and the fact that Amber now supports netCDF format makes that
information obsolete.

I would output netCDF from ptraj and give it a try, at least.

Also, the webpage I mentioned is not the same as the one listed on the
nmoldyn2 web page.
I googled for "ACO" and "AmberReader" to find http://awe.mol.uj.edu.pl/~murzyn/convert/convert.html
  which DOES work.

You can find historical versions of the other page at the Internet
Archive Wayback Machine, which indicates that the old page was last
updated in December 2004, so I would think that it is simply just old
information.
By the way, the "new" page was last updated in April of 2005.

A short perusal of the netCDF mailing list at www.unidata.ucar.edu
indicates that the authors of AMBER did not support netCDF until the
spring of 2006.

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