VMD-L Mailing List

From: Kalavera_at_gmx.net
Date: Thu Apr 02 2009 - 09:58:53 CDT

Problem solved:
After watching my PDB-file in detail again there came up an unusually entry in every row, e.g.:

ATOM 43808 CLA CLA 33 24.508 4.158 -53.556 1.00 0.00 ION CL

The last entry "CL" caused the trouble. If I use this line :

ATOM 43808 CLA CLA 33 24.508 4.158 -53.556 1.00 0.00 ION

the ions are both the same size.
Thx for the support, Axel

your M.Kalavera

-------- Original-Nachricht --------
> Datum: Thu, 02 Apr 2009 10:25:33 -0400
> Von: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
> An: Kalavera_at_gmx.net
> CC: vmd-l_at_ks.uiuc.edu
> Betreff: Re: vmd-l: Problem with autoionize ?

> On Thu, 2009-04-02 at 15:50 +0200, Kalavera_at_gmx.net wrote:
> > hello everybody,
> > after using the autoionize script from Ilya Balabin and Marcos Sotomayor
> > (http://www.ks.uiuc.edu/Research/vmd/plugins/autoionize/)and exchanging
> the sodium with potassium I got confused by the visual results in VMD,
> because of different radii for potassium and chloride ions.
> > In my case the chloride ion is displayed nearly two times smaller than
> the potassium if VDW is used as the drawing method. I need to know if this
> is the normal case and whether my system is setup properly.
>
> unless you use a file format that contains explicit radii,
> VDW uses covalent radii from an internal table. those have
> no idea that you have ions. in general, you have to keep in
> mind that VMD knows only what is provided. it deliberately
> does not know any chemistry.
>
> cheers,
> axel.
>
> > Thx for your replies,
> > M.Kalavera
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot. 

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