VMD-L Mailing List

From: Brian Radak (radak004_at_umn.edu)
Date: Wed Jul 25 2012 - 08:45:38 CDT

Hi all,

I'm not an official emissary of the AMBER community or anything, but the
users here (in two of the main development groups) have mostly taken to
using the rst7 file extension exclusively. In my experience this causes
VMD to load any and all AMBER mdcrd format variants properly, although
John's post indicates that I might be mistaken. I don't think I know anyone
who tries to load with the AMBER coordinates or AMBER coordinates + box
options (at least intentionally); would it be worthwhile to consider
changing VMD's behavior to recognize files with the crd extension as being
in AMBER7 Restart format? Are there other file formats that use the crd and
rst file extensions (like from Gromacs or Tinker) that would make this
problematic?

It is perhaps interesting that this problem does not seem occur with the
change from the old (pre-AMBER7) to new AMBER prmtop format (post-AMBER7 or
parm7). The changes were either so minor that the new format is still read
just fine or else files with prmtop extension are recognized as being in
parm7 format.

Regards,
Brian

On Tue, Jul 24, 2012 at 4:36 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Tom,
> The problem here is that the Amber tools use slightly inconsistent
> variations of their file formats depending on which program reads/writes
> them, and there's no way to differentiate which kind of file it is while
> loading it due to the relatively unstructured way that they are organized,
> so the user has to select the correct plugin to read the type of file
> they are using...
>
> Cheers,
> John
>
> On Tue, Jul 24, 2012 at 03:24:15PM -0500, Thomas C. Bishop wrote:
> > glad to help but we haven't let John Stone know if there's a bug
> > someplace or if this is just a labeling/usage issue w/ VMD.
> > IN any case -rst7 seems to do the trick.
> >
> > TOm
> >
> > On 07/24/2012 12:38 PM, Mahendra B Thapa wrote:
> > >Dear Dr. John and Dr.Thomas
> > >
> > >
> > > I am able to load my amber 12 generated mdcrd file
> > >in VMD with " file type - AMBER7 Restart" [suggested by Dr.Thomas,
> > >www.latech.edu/~bishop <http://www.latech.edu/%7Ebishop>] instead of
> "Amber coordinates with periodic
> > >box" .
> > >
> > >Thank you for the help,
> > >Mahendra Thapa
> > >
> > >
> > >On Mon, Jul 2, 2012 at 4:22 PM, Thapa, Mahendra (thapamb)
> > ><thapamb_at_mail.uc.edu> wrote:
> > >>
> > >>
> > >>________________________________________
> > >>From: John Stone
> > >>Sent: Monday, July 02, 2012 2:22:10 PM (UTC-06:00) Central America
> > >>To: Thapa, Mahendra (thapamb)
> > >>Cc: vmd-l_at_ks.uiuc.edu
> > >>Subject: Re: vmd-l: difficulty in viewing AMBER mdcrd files
> > >>
> > >>Hi,
> > >> Can you post a gzipped copy of your file so I can try loading it?
> > >>
> > >>Cheers,
> > >> John Stone
> > >> vmd_at_ks.uiuc.edu
> > >>
> > >>On Mon, Jul 02, 2012 at 12:56:43PM -0400, Mahendra B Thapa wrote:
> > >>> Dear VMD users,
> > >>>
> > >>> I generated amber mdcrd file using
> > >>> amber 12
> > >>> with the amber force field. To view the structure, I at first
> loaded
> > >>> prmtop file with "file type - AMBER7 Parm" and then loaded mdcrd
> > >>> file with
> > >>> " file type - Amber coordinates with periodic box". Unfortunately,
> > >>> VMD did
> > >>> not produce image instead just a line like image. Interestingly
> > >>> when I
> > >>> used the pdb- format , it worked fine. The question is: why VMD
> > >>> looks like
> > >>> not supporting prmtop and mdcrd files.
> > >>>
> > >>> Thanks,
> > >>> Mahendra Thapa
> > >>> University of Cincinnati
> > >>--
> > >>NIH Resource for Macromolecular Modeling and Bioinformatics
> > >>Beckman Institute for Advanced Science and Technology
> > >>University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > >>http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > >>http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
> > >>
> > >>
> > >
> >
> >
> > --
> > *******************************
> > Thomas C. Bishop
> > Tel: 318-257-5209
> > Fax: 318-257-3823
> > www.latech.edu/~bishop <http://www.latech.edu/%7Ebishop>
> > ********************************
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
> 

-- 
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 Brian Radak                                             :     BioMaPS
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