VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 18 2011 - 16:14:00 CDT

Craig,
  Can you send me a few gzipped MDF files so I can do some local testing?
This plugin was originally written in 2003/2004 back when there were still
a couple of people on site using InsightII, but since then it hasn't had very
much attention other than little bug fixes. Since nobody here uses
InsightII or related software anymore, I don't even have any MDF files
available for testing. If you can send me a few, that'd be very helpful.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Apr 18, 2011 at 02:03:51PM -0400, Craig Knox wrote:
> Dear VMD Developers:
>
> First of all, thank you very much for such a wonderfully useful and
> powerful code!
>
> FYI, I believe there's a minor bug in the mdf molfile plugin that
> causes the element symbol field to be incorrectly used in place of the
> atom type (FF) field.
>
> Here's the relevant piece of code (lines 62-66) from
> plugins/molfile_plugin/src/mdfplugin.C:
>
> static int read_mdf_structure_line(molfile_atom_t *atom, const char *line) {
> // Read pertinent structure information from the line
> if ( sscanf(line, "%[^:]:%s %s %*s %*s %*d %*s %f %*d %*d %*d %f",
> atom->resname, atom->name, atom->type,
> &atom->charge, &atom->occupancy) != 5 ) {
>
> The sscanf line (line 64) should be changed to:
> if ( sscanf(line, "%[^:]:%s %*s %s %*s %*d %*s %f %*d %*d %*d %f",
>
> , in order to skip the element field and read the atom_type field instead.
>
> As an example, here's the beginning of my mdf file:
>
> !BIOSYM molecular_data 4
>
> !Date: Wed Jan 12 17:19:39 2011 Materials Studio Generated MDF file
>
> #topology
>
> @column 1 element
> @column 2 atom_type
> @column 3 charge_group
> @column 4 isotope
> @column 5 formal_charge
> @column 6 charge
> @column 7 switching_atom
> @column 8 oop_flag
> @column 9 chirality_flag
> @column 10 occupancy
> @column 11 xray_temp_factor
> @column 12 connections
>
> @molecule Dendrimer
>
> LAYE_1:N1 N n3 ? 0 0 -0.5610 0 0 8 1.0000
> 0.0000 C1 C21H_2:C21 C21H_3:C21
>
> In VMD,
>
> vmd > set a1 [atomselect top "index 0"]
> atomselect1
> vmd > $a1 get {index name type element atomicnumber}
> {0 N1 N X -1}
>
> So, the molfile plugin read the 2nd field ('N') as the atom type
> instead of the 3rd field ('n3').
>
> Notice that this bug is likely due to the misleading header/comment in
> the mdf file, which says "@column 2 atom_type", although this seems to
> be counting from zero, not one (i.e., there's an implicit "@column 0
> resname_resid:name").
>
> Is there any reason to use the element field in place of the
> atom_type, or is this a bug?
>
> Thanks,
> Craig
>
> ---
>
> Craig K. Knox, Ph.D.
>
> Computational Materials Science
>
> U.S. Army Research Laboratory
> Materials & Manufacturing Science Division
> Macromolecular Science & Technology Branch
> 4600 Deer Creek Loop
> RDRL-WMM-G, Bldg. 4600, Rm. C237
> Aberdeen Proving Ground, MD 21005-5069
> 410-306-0856 (phone)
> 410-306-0676 (fax)
> craig.knox_at_us.army.mil
> craig.k.knox_at_gmail.com 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078