VMD-L Mailing List

From: Cosseddu, Salvatore (S.M.Cosseddu_at_warwick.ac.uk)
Date: Sun Jan 22 2012 - 15:27:30 CST

Dear Elia

If you use AUTOPSF I presume you are using CHARMM FF. If you are interested in using as VdW radii the R_min/2 parameters, take a look to
https://github.com/s-cosseddu/VMD-scripts
It's the test folder I made when I was first setting github. It happened that in those days I was working on a parser for CHARMM FF par files. This is the only script you will find there (I had no time to upload more).

The version uploaded on github does exactly what I said before: put Rmin/2 from your FF file (CHARMM format) in the VMD radius field for each atom.

Usage: from TkConsole

source parseCHARMMpar.tcl
::parseCHARMMpar::VdWassign <molID> <CHARMM parameter file>

molID could be "top" (i.g. if there is only one loaded molecule) or the number on the left of the loaded molecule on the VMD main window.

try if it helps

Regards
    

--
Salvatore Cosseddu
PhD student
Centre for Scientific Computing and School of Engineering
University of Warwick
Coventry CV4 7AL
United Kingdom
email: S.M.Cosseddu_at_warwick.ac.uk
-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu on behalf of Zumot, Elia Nabil
Sent: Sat 21/01/2012 01:55
To: John Stone
Cc: Axel Kohlmeyer; vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: ionic radii of sodium and chloride
 
Hi John,
All my pdb and psf files were generated with VMD(1.8.7 or 1.9) and the AutoPSF plugin.
Also, all my simulations were run by NAMD (2.7 or 2.8) (thus, dcd and restart.coor files). 
resnames here are SOD and CLA.
I'm assuming the values that you will tell me about are the ones that will be multiplied by the scaling factor set by the user in the "sphere scale" in the "graphical representations" window for display?
And if use the tcl command:
$sel set radius 1.0 
Does this mean a radius of 1 Angstrom or a scaling of 1?
Thanks a lot
Elia
Elia Zomot, PhD
Computational and Systems Biology Department
School of Medicine, University of Pittsburgh
3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
Voice: 412 624 8699 - Fax: 412 648 3163
enz1_at_pitt.edu
________________________________________
From: John Stone [johns_at_ks.uiuc.edu]
Sent: Friday, January 20, 2012 3:05 PM
To: Zumot, Elia Nabil
Cc: Axel Kohlmeyer; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: ionic radii of sodium and chloride
Hi Elia,
  The way VMD assigns atomic properties (e.g. radii, masses, etc) depends
greatly upon what file formats you used when you loaded the structure into
VMD.  Some file formats provide VMD with explicit values for all of the
key atomic properties, other file formats provide nothing but the atom
name and coordinates.  In the cases where the files loaded do not contain
an atomic property such as the radius, VMD has to "guess" this information
using some combination of the atomic properties that the file does specify.
Some VMD molecule file reader plugins also contain their own atomic
property lookup tables because they are able to do a better job at guessing
than VMD can because they have access to file-format-specific details that
VMD doesn't know about.  So, the particular strategy that is used for a given
structure depends directly on the details of what files you loaded, what
file formats they were stored in, and what information was contained therein.
If you me us more about what files you're loading, I can tell you how the
radii are getting assigned.
Axel's suggestion is a simple way to address the immediate problem by
overriding the auto-assigned radii with an atom selection command.
Cheers,
  John
On Fri, Jan 20, 2012 at 11:57:19AM -0500, Zumot, Elia Nabil wrote:
> Thank you Axel.
>
> Could you direct me to the file that contains the atomic radii that are displayed in VMD?
>
> (I have found the PeriodicTable.C file but it contains the correct ionic radii)
>
> Best
>
> Elia
>
>
>
>
> Elia Zomot, PhD
> Computational and Systems Biology Department
> School of Medicine, University of Pittsburgh
> 3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
> Voice: 412 624 8699 - Fax: 412 648 3163
> enz1_at_pitt.edu
> ________________________________________
> From: Axel Kohlmeyer [akohlmey_at_gmail.com]
> Sent: Thursday, January 19, 2012 10:12 PM
> To: Zumot, Elia Nabil
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: ionic radii of sodium and chloride
>
> On Jan 19, 2012, at 10:03 PM, "Zumot, Elia Nabil" <enz1_at_pitt.edu> wrote:
>
> > Dear VMDers,
> >
> > Any reason why VMD shows sodium ions to be bigger than chloride when it should be the other way around?
> >
> > In crystals the radius of Na+ is 0.095 nm and that of Cl-  0.181 nm.
> >
>
> That is because VMD cannot tell the difference between an element and
> an ion or a chlorine or chloride and a carbon.
>
> If you don't like VMD's choices you can always write a little script
> that changes it or use a file format that does contain the radius
> information in a way that VMD supports reading it.
>
> VMD is very deliberately a very dumb and ignorant software that relies
> on you to provide it with the proper information. It does not even try
> to be smart (for the most part, that is).
>
> Axel
>
>
>
> >
> > Thanks
> >
> > Elia Zomot
> >
> >
> >
> > Elia Zomot, PhD
> > Computational and Systems Biology Department
> > School of Medicine, University of Pittsburgh
> > 3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
> > Voice: 412 624 8699 - Fax: 412 648 3163
> > enz1_at_pitt.edu
--
NIH Resource 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/       Fax: 217-244-6078