VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jul 20 2007 - 00:02:24 CDT

On Thu, 19 Jul 2007, Arneh Babakhani wrote:

arneh,

AB> Hi,
AB>
AB> I have a pdb file, that I convert to a pdbqt using AutoDock.
AB>
AB> I'm trying to read in this pdbqt file into VMD. (at the command line, I'm
AB> just entering 'vmd Molecule.pdbqt').
AB>
AB> But VMD isn't displaying the entire molecule (is it confused by the
AB> 'BRANCH' line in the pdbqt???).

most likely. there is no direct support for .pdbqt files, so
VMD (or more precisely the molfile library) falls back to the
default format (which is .pdb). now as you already noticed,
the .pdbqt is _not_ a standard .pdb file. VMD does the best
it can, but at some point it fails...

cheers,
   axel.

AB>
AB> I've pasted the pdbqt below, and attached the files.
AB>
AB> Thanks,
AB>
AB> Arneh
AB>
AB>
AB> REMARK 1 active torsions:
AB> REMARK status: ('A' for Active; 'I' for Inactive)
AB> REMARK 1 A between atoms: A5_3 and C1_8
AB> ROOT
AB> ATOM 1 C1 EPA 2 -3.086 0.090 1.171 1.00 0.00 0.052
AB> ATOM 2 C3 EPA 2 -3.033 0.853 2.533 1.00 0.00 0.195
AB> ATOM 3 N5 EPA 2 -2.941 -0.245 3.498 1.00 0.00 -0.066
AB> ATOM 4 H6 EPA 2 -2.123 -0.836 3.333 1.00 0.00 0.278
AB> ATOM 5 H7 EPA 2 -2.985 0.088 4.464 1.00 0.00 0.278
AB> ATOM 6 C8 EPA 2 -4.398 1.477 2.926 1.00 0.00 0.036
AB> ATOM 7 C11 EPA 2 -5.220 0.225 3.307 1.00 0.00 0.035
AB> ATOM 8 C14 EPA 2 -4.182 -0.902 3.087 1.00 0.00 0.187
AB> ATOM 9 C16 EPA 2 -3.904 -1.169 1.587 1.00 0.00 0.044
AB> ENDROOT
AB> BRANCH 1 10
AB> ATOM 10 A5 EPA 1 -1.797 -0.269 0.494 1.00 0.00 -0.034
AB> ATOM 11 A3 EPA 1 -1.838 -0.771 -0.830 1.00 0.00 0.012
AB> ATOM 12 A7 EPA 1 -0.520 -0.156 1.096 1.00 0.00 0.126
AB> ATOM 13 A1 EPA 1 -0.659 -1.121 -1.513 1.00 0.00 0.045
AB> ATOM 14 A11 EPA 1 0.574 -0.972 -0.856 1.00 0.00 0.125
AB> ATOM 15 c EPA 1 2.028 -1.371 -1.619 1.00 0.00 -0.062
AB> ATOM 16 N9 EPA 1 0.602 -0.501 0.415 1.00 0.00 -0.248
AB> ENDBRANCH 1 10
AB> TORSDOF 1
AB> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.