AMBER Archive (2009)

Subject: Re: [AMBER] nmoldyn2 with Amber

From: M. L. Dodson (activesitedynamics_at_comcast.net)
Date: Sun Mar 08 2009 - 13:32:22 CDT

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?

Bud Dodson

> >
> >
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-- 
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one

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