VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 03 2002 - 09:39:22 CDT

Hi Ran,
  It depends greatly on what type of structure file you are
loading. In absence of this information from the structure files
that are loaded, VMD "guesses" based on the string atom names.
The simple heuristic that does the "guessing" about atom types
is shown below:

// return a 'default' value for a given atom name
float BaseMolecule::default_radius(char *nm) {
  float val = 1.5;
  // some names start with a number
  while (*nm && isdigit(*nm))
    nm++;
  if(nm) {
    switch(toupper(nm[0])) {
      case 'H' : val = 1.00f; break;
      case 'C' : val = 1.50f; break;
      case 'N' : val = 1.40f; break;
      case 'O' : val = 1.30f; break;
      case 'F' : val = 1.20f; break;
      case 'S' : val = 1.90f; break;
    }
  }

  return val;
}

On Thu, Oct 03, 2002 at 04:33:30PM +0200, ran friedman wrote:
> Hi,
>
> Any ideas where can I find the VDW radii that VMD assigns to atoms?
>
> Ran.
>
> ------------------------------------------------------
> Ran Friedman
> Laser laboratory for fast reactions in biology
> Department of biochemistry
> Faculty of life sciences
> Tel-Aviv university
> 972-3-6409824
> ------------------------------------------------------ 

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