VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Thu Jul 19 2007 - 18:01:01 CDT

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