VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Sep 12 2010 - 14:59:54 CDT

On Sun, 2010-09-12 at 20:18 +0200, Meyer-Almes, Franz-Josef, Prof. Dr.
wrote:
> Dear all,

dear franz,

> 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.

right. same here.

> 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?

yes. the reason for this is that the .gro file does
not contain any bonding information, so VMD would have
to guess. this kind of guess is very difficult, since
there is no indication that atom BR1 is a bromium atom.
however, knowing the element determined the radius to
be used when guessing the bonding structure.

the element guessing in VMD is based on PDB naming
conventions, where the second letter indicates the
position in the residue. thus in this case the guess
is likely to be wrong.

the remedy is to correct the information. this can be
done with a vmd script or some commands typed interactively.
for example like this:

set sel [atomselect top {name "BR.*"}]
$sel set element Br
$sel set radius 1.85
mol bondsrecalc top

you may have to trigger a full redraw, e.g. by
changing the representation to see the new bond.

cheers,
    axel.

>
>
> 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
>
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.