VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Apr 11 2015 - 12:47:02 CDT

Hi,
  You could write a script to load the VdW radii from the
parameter files, and this could probably done pretty easily using
the existing "readcharmmpar" plugin. The readcharmmpar plugin was
originally developed for use by the older "paratool" force field
parameterization plugin. It doesn't have any user docs unfortunately
because the author never got around to it, but I would suggest reading
the code and you can probably find a way to call
::Pararead::read_charmm_parameters and ::Pararead::getvdwparam
in some combination to get this information, perhaps with a few
extra routines of your own.

The source code for readcharmmpar is in vmd/plugins/noarch/tcl/readcharmmpar1.2/
where 'vmd' is the installation directory of VMD.
You can query that location like this in a running VMD:
  package require readcharmmpar
  puts "readcharmmpar dir: $env(CHARMMPARDIR)"

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Apr 11, 2015 at 12:22:42AM -0700, Gianluca Interlandi wrote:
> Dear list,
>
> It is my understanding that VMD guesses the atoms' VDW radii based
> on the atom string names. Is there a way to load the VDW radii from
> the parameter files, e.g., par_all22_prot.inp? I tried loading the
> PSF but even that does not contain the VDW radii.
>
> Thanks,
>
> Gianluca
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Research Assistant Professor at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> ----------------------------------------------------- 

-- 
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Beckman Institute for Advanced Science and Technology
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http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/