VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 20 2007 - 13:27:53 CDT

The molfile plugins (plugins that read/write atomic structures,
trajectories, potential maps, etc) are currently all written in
C or a portable subset of C++. The first step in writing a plugin is
to read the plugin programmer's guide for an introduction to the process:
  http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 20, 2007 at 10:35:24AM -0700, Arneh Babakhani wrote:
> Ok, thanks, yes I do think it would be useful, what's the process of
> writing a plugin? what do you have to code in?
> >
> > Arneh,
> > We don't have a reader for Autodock's "pdbqt" format, but if
> > a lot of people would find it very useful to be able to load them
> > a pdbqt plugin could be written. Even better, if someone familiar
> > with pdbqt wants to write the plugin, I can give guidance and help
> > them get it done... :-)
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Thu, Jul 19, 2007 at 04:01:01PM -0700, Arneh Babakhani wrote:
> >> Hi,
> >>
> >> I have a pdb file, that I convert to a pdbqt using AutoDock.
> >>
> >> I'm trying to read in this pdbqt file into VMD. (at the command line,
> >> I'm
> >> just entering 'vmd Molecule.pdbqt').
> >>
> >> But VMD isn't displaying the entire molecule (is it confused by the
> >> 'BRANCH' line in the pdbqt???).
> >>
> >> I've pasted the pdbqt below, and attached the files.
> >>
> >> Thanks,
> >>
> >> Arneh
> >>
> >>
> >> REMARK 1 active torsions:
> >> REMARK status: ('A' for Active; 'I' for Inactive)
> >> REMARK 1 A between atoms: A5_3 and C1_8
> >> ROOT
> >> ATOM 1 C1 EPA 2 -3.086 0.090 1.171 1.00 0.00
> >> 0.052
> >> ATOM 2 C3 EPA 2 -3.033 0.853 2.533 1.00 0.00
> >> 0.195
> >> ATOM 3 N5 EPA 2 -2.941 -0.245 3.498 1.00 0.00
> >> -0.066
> >> ATOM 4 H6 EPA 2 -2.123 -0.836 3.333 1.00 0.00
> >> 0.278
> >> ATOM 5 H7 EPA 2 -2.985 0.088 4.464 1.00 0.00
> >> 0.278
> >> ATOM 6 C8 EPA 2 -4.398 1.477 2.926 1.00 0.00
> >> 0.036
> >> ATOM 7 C11 EPA 2 -5.220 0.225 3.307 1.00 0.00
> >> 0.035
> >> ATOM 8 C14 EPA 2 -4.182 -0.902 3.087 1.00 0.00
> >> 0.187
> >> ATOM 9 C16 EPA 2 -3.904 -1.169 1.587 1.00 0.00
> >> 0.044
> >> ENDROOT
> >> BRANCH 1 10
> >> ATOM 10 A5 EPA 1 -1.797 -0.269 0.494 1.00 0.00
> >> -0.034
> >> ATOM 11 A3 EPA 1 -1.838 -0.771 -0.830 1.00 0.00
> >> 0.012
> >> ATOM 12 A7 EPA 1 -0.520 -0.156 1.096 1.00 0.00
> >> 0.126
> >> ATOM 13 A1 EPA 1 -0.659 -1.121 -1.513 1.00 0.00
> >> 0.045
> >> ATOM 14 A11 EPA 1 0.574 -0.972 -0.856 1.00 0.00
> >> 0.125
> >> ATOM 15 c EPA 1 2.028 -1.371 -1.619 1.00 0.00
> >> -0.062
> >> ATOM 16 N9 EPA 1 0.602 -0.501 0.415 1.00 0.00
> >> -0.248
> >> ENDBRANCH 1 10
> >> TORSDOF 1
> >
> >
> >
> >
> > --
> > 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
> > 

-- 
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