VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 07 2021 - 16:48:16 CDT

Hi Ali,
  It is worth noting that the text in that section of the VMD docs was
only meant to be exemplary, and there's no way I (or anyone) wants
to read a page that lists all 75+ file formats and their intricate
details. In the context what is meant by "native" file formats,
as Axel already pointed out, anything that has a built-in plugin
is read "natively". The only exceptions (non-native) are files that
are translated on the fly from formats VMD doesn't understand,
by using something like Babel or OpenBabel.

Best,
  John

On Wed, Apr 07, 2021 at 05:34:57PM -0400, Axel Kohlmeyer wrote:
> On Wed, Apr 7, 2021 at 5:19 PM Ali Osman Acar <aliosmanacar1897_at_gmail.com>
> wrote:
>
> > Hi Axel,
> > The native part doesn't change in time I guess. This is the 1.9.4
> > documentation and still same after 20 years. :D
> >
>
> *all* "native" file formats that VMD can read is through the molfile plugin
> library. like I already stated, there is no difference.
> that specific file of the documentation has apparently not been updated in
> ages.
>
> ..and setting the file type explicitly should not be needed. it is not for
> me (see below).
>
> axel.
>
> vmd > mol new full.psf waitfor all
> Info) Using plugin psf for structure file full.psf
> psfplugin) no cross-terms defined in PSF file.
> Info) Analyzing structure ...
> Info) Atoms: 3072
> Info) Bonds: 0
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 3072
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 3072 Protein: 0 Nucleic: 0
> 1
> vmd > mol addfile full.lammpstrj waitfor all
> lammpsplugin) New style dump with 6 data fields. Coordinate data flags: 0x01
> lammpsplugin) Using absolute atomic coordinates directly.
> Info) Using plugin lammpstrj for coordinates from file full.lammpstrj
> Info) Finished with coordinate file full.lammpstrj.
> 1
> vmd > vmdinfo version
> 1.9.4a51
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!ppb89qVlw71cIzj_OKe82rK3DWAP58Nx4Nb7RtwDpt_wHlROnH5_0hovOlkDHBscDw$
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
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/