VMD-L Mailing List

From: Salomon Turgman Cohen (sturgman_at_gmail.com)
Date: Wed Aug 20 2014 - 13:19:32 CDT

Hey Rafal,

If I understand what you are asking, a possible solution is to select the
relevant atoms by index number and set the representation style to dynamic
bonds.

You can do this by:

1. Select graphics->representation
2. Click "Create Rep"
3. On the "Selected Atoms" text box type something like "index 0 1 2" where
0 1 2 would be replaced by the index of the actual atoms of interest.
4. Select DynamicBonds from the "Drawing Method" selection box.
5. Adjust the cutoff until you see the bonds that you want.

This would be tedious if the index of the atoms is changing or if you have
to do this for many molecules!

Salomon

On Wed, Aug 20, 2014 at 11:26 AM, Rafał Gąsior <raf.gsior90_at_gmail.com>
wrote:

> Dear all,
>
> I am writing my Master's thesis about the aging of biomaterials. I need to build
> a model of elastin fibers. The fiber is made up of individual particles,
> which are bonded. This bond is demosine, which is formed of one lysine and
> three allysine derived from 4 different peptide chains. At this point, I
> have a problem. I do not know how to use the program vmd can connect four
> molecules in one and specifically identify the atoms that are to build a
> bond.
>
> Thanks a lot in advance for your help,
> Rafał
> 

-- 
Salomon Turgman Cohen
Assistant Professor
Chemical Engineering
Kettering University
(919) 341-9650