VMD-L Mailing List

From: Meyer-Almes, Franz-Josef, Prof. Dr. (franz-josef.meyer-almes_at_h-da.de)
Date: Sun Sep 12 2010 - 13:18:46 CDT

Dear all,

I use VMD 1.8.7 under Windows XP.
When I load the following .gro file, the bromo atom is depicted as a tiny single point and not connected to the aromatic C2 atom as it should. The distance is not too far from the expected distance between a bromo atom and the corresponding C atom.
After energy minimization of the drug molecule the distance between BR1 and C2 is 1.89 Angstrom. Even the minimized structure is not depicted correctly.

Do you have a remedy for the observed behaviour?

Thank you in advance,

Franz

Drg.gro:

PRODRG COORDS
   21
    1DRG C1 1 8.555 5.270 -3.838
    1DRG C2 2 8.529 5.317 -3.967
    1DRG BR1 3 8.392 5.231 -4.068
    1DRG C3 4 8.602 5.424 -4.019
    1DRG O1 5 8.580 5.472 -4.145
    1DRG HAA 6 8.507 5.419 -4.189
    1DRG C4 7 8.700 5.485 -3.941
    1DRG C5 8 8.725 5.438 -3.812
    1DRG C6 9 8.653 5.331 -3.760
    1DRG C7 10 8.681 5.281 -3.619
    1DRG C8 11 8.788 5.172 -3.616
    1DRG N1 12 8.913 5.205 -3.598
    1DRG O2 13 8.945 5.341 -3.583
    1DRG HAB 14 9.044 5.351 -3.570
    1DRG C9 15 8.736 5.032 -3.632
    1DRG O3 16 8.619 5.004 -3.652
    1DRG N2 17 8.828 4.932 -3.624
    1DRG HAD 18 8.925 4.956 -3.626
    1DRG C10 19 8.790 4.792 -3.610
    1DRG C11 20 8.903 4.690 -3.629
    1DRG S1 21 8.838 4.520 -3.654
   1.11480 1.11480 1.11480

Prof. Dr. F.-J. Meyer-Almes

Hochschule Darmstadt

Fachbereich Chemie- und Biotechnologie

Schnittspahnstr. 12

64287 Darmstadt

Email: franz-josef.meyer-almes_at_h-da.de

Tel.: +49-(0)6151-168406

http://www2.h-da.de/cub/index.php?id=177