VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Wed Jul 25 2012 - 11:40:35 CDT

Thanks Brian,
This is the sort of "common practices" advice that I like to hear.
Cheers,
Tom

On 07/25/2012 08:45 AM, Brian Radak wrote:
> 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
> <mailto: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 <mailto: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 <mailto: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 <mailto: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/
> <http://www.ks.uiuc.edu/%7Ejohns/> Phone: 217-244-3349
> <tel:217-244-3349>
> > >>http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
> <tel:217-244-6078>
> > >>
> > >>
> > >
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for
> Integrative Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004_at_umn.edu <mailto:radak004_at_umn.edu>
> : radakb_at_biomaps.rutgers.edu
> <mailto:radakb_at_biomaps.rutgers.edu>
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute
> appropriate address.
> 

-- 
*******************************
    Thomas C. Bishop
     Tel: 318-257-5209
     Fax: 318-257-3823
    www.latech.edu/~bishop
********************************