VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 28 2004 - 09:55:29 CDT

Manuel,
  VMD is forced to "guess" various atom information in absence of
file formats that provide this information. At present, only
PSF, and PARM files provide mass and charge information, for example.
VMD has a very small lookup table for a few common atoms, when a PSF
or PARM file is not supplied, but as you've discovered, this doesn't
cover the entire periodic table, nor the alternate atom names used by
various simulation packages. You can use a simple script to set the atomic
properties for atoms that aren't correctly recognized by VMD when using
a file format that doesn't provide this information. Let us know if you
need more help with this.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Sep 28, 2004 at 02:55:44PM +0200, Manuel Rueda wrote:
> Dear VMD list,
> I was testing and modifying some tcl scripts that use the mass of the
> atoms for calculating some properties ( radius of gyration, moments of inertia ) and
> I realized that that the mass of the phosphate in the vector WEIGHTS is
> equal to 12 and no to 31. Is this a constant value for some "strange"
> atoms?
>
> Best regards
>
>
> --
> ---------------------------------------------------------------------------
> Manuel Rueda e-mail: manu_at_mmb.pcb.ub.es
> Molecular Modelling & Bioinformatics phone: + 34 93 403 71 55
> IRBB, Parc Cientific de Barcelona Fax : + 34 93 403 71 57
> C/Josep Samitier 1-5, 08028 Barcelona 

-- 
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