VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Apr 11 2015 - 12:47:02 CDT
- Next message: John Stone: "Re: using namdstats.tcl"
- Previous message: Michael Patzschke: "Re: Mac issue"
- In reply to: Gianluca Interlandi: "Read CHARMM VDW radii into VMD"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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.
> -----------------------------------------------------
-- 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/
- Next message: John Stone: "Re: using namdstats.tcl"
- Previous message: Michael Patzschke: "Re: Mac issue"
- In reply to: Gianluca Interlandi: "Read CHARMM VDW radii into VMD"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]