VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 16 2015 - 10:03:41 CDT

Hi,
  I know for sure we don't have a way to read the Yasara output you're
describing in VMD currently. If the Yasara authors wanted to contribute
a VMD plugin to read their .sim format, we'd be happy to have it.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 16, 2015 at 11:56:54AM -0300, Daniela Rivas wrote:
> Yes, I did. I'm waiting for their answer. Thank you.
> 2015-06-16 11:49 GMT-03:00 Axel Kohlmeyer <[1]akohlmey_at_gmail.com>:
>
> On Tue, Jun 16, 2015 at 10:46 AM, Daniela Rivas
> <[2]dani.rivas.r_at_gmail.com> wrote:
> > I'm using Yasara to run molecular dynamics and the output file for the
> > trajectories is in .sim format. I have no idea what it contains, I
> tried to
> > find out and I couldn't find anything.
>
> how about asking the authors of that software?
> axel.
> >
> > Thanks!
> >
> > 2015-06-16 11:38 GMT-03:00 Axel Kohlmeyer <[3]akohlmey_at_gmail.com>:
> >>
> >> On Tue, Jun 16, 2015 at 10:02 AM, Daniela Rivas
> <[4]dani.rivas.r_at_gmail.com>
> >> wrote:
> >> > Hi,
> >> >
> >> > Is it possible to load a trajectory file in VMD using the .sim
> format?
> >> > If
> >> > not, what can I do? Should I convert it to another format?
> >>
> >> what program does generate a .sim file? how is the format defined?
> >>
> >> VMD supports different file format through plugins. the list of
> >> available plugins is given here. you'll have to check if there is
> >> anything that is compatible with the file you have.
> >> [5]http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/
> >>
> >> since i don't know what a .sim file contains and how it is created, i
> >> cannot give any advice. if there is no suitable plugin, you can see
> if
> >> there is a converter that outputs a supported file format (caution,
> >> this may lose information). otherwise, there is always the option of
> >> writing a custom plugin to support this particular file format. that
> >> would also help other users of the same program.
> >>
> >> axel.
> >>
> >> >
> >> > I hope you can help me.
> >> >
> >> > Thanks!
> >> > Daniela.
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer [6]akohlmey_at_gmail.com [7]http://goo.gl/1wk0
> >> College of Science & Technology, Temple University, Philadelphia PA,
> USA
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >
> >
>
> --
> Dr. Axel Kohlmeyer [8]akohlmey_at_gmail.com [9]http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
> References
>
> Visible links
> 1. mailto:akohlmey_at_gmail.com
> 2. mailto:dani.rivas.r_at_gmail.com
> 3. mailto:akohlmey_at_gmail.com
> 4. mailto:dani.rivas.r_at_gmail.com
> 5. http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/
> 6. mailto:akohlmey_at_gmail.com
> 7. http://goo.gl/1wk0
> 8. mailto:akohlmey_at_gmail.com
> 9. http://goo.gl/1wk0 

-- 
NIH Center 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/