VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 20 2007 - 11:27:39 CDT

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
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