VMD-L Mailing List

From: Ziemys, Arturas (Arturas.Ziemys_at_uth.tmc.edu)
Date: Fri Apr 09 2010 - 15:34:09 CDT

If I load a plain PDB file and do as you have suggested, how to access the binding information after ?

Arturas

From: Axel Kohlmeyer [akohlmey_at_gmail.com]
Sent: Friday, April 09, 2010 3:23 PM
To: Ziemys, Arturas
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: DynamicBonding

On Fri, Apr 9, 2010 at 3:10 PM, Ziemys, Arturas
<Arturas.Ziemys_at_uth.tmc.edu> wrote:
> Hi,
>
> Is there any way access "DynamicBonding' information ? For example, to save to PDB with CONNECT records, or MOL2. Can I access by script ?

you can actually do better. the Dynamic Bonds representation has a fixed cutoff
for all atom distances.

if you do:

mol bondsrecalc [molinfo top]

VMD will recalculate your bonding information based on
atom dependent (covalent) atomic radii (initially from an internal table,
but you can reset them). that will sort out all kinds of issue for bonding
with atoms of largely differing radius.

cheers,
    axel.

> Arturas
>
> 

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