VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 24 2012 - 15:36:01 CDT

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] 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
> ******************************** 

-- 
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