VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Fri Jul 20 2007 - 09:19:00 CDT

Ok great, thanks, that's what I suspected. just wanted to make sure I
wasn't missing something,

Arneh

> 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
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>