VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Oct 21 2009 - 12:58:15 CDT

On Wed, Oct 21, 2009 at 12:36 PM, Elias Ahadi <eahadi_at_uwo.ca> wrote:
> Hello,
>
> I am working on a project in which I am modeling a protein chain where each unit is 4.0 A apart. My question is how come VMD (v1.8.7) does not display the bond connectivity for such a simple model protein. Below is the model protein chain in question in PDB format.

VMD for the most part relies on guessing bonds based on distance when
loading .pdb files.
it will accept additional records only, if the whole pdb file is
conforming to some minimal
conditions. yours is obviously not fully standard conforming, so i
would guess, that the
CONECT records get ignored. to make a more qualified statement, one
would have to
look at the .pdb format parser in a debugger and follow the parsing
process to see where
it bails out.

> If anyone knows of a technique that can be used to display the bonds in VMD, I would really appreciate it.

there are many file formats that can reliably store bonds, like .psf.
also you can easily set any
kind of bond from script level by creating an atom selection and using
the setbonds/getbonds
mechanism. if that is too complicated, you could use the front end
scripts in the topotools plugin.

if you look at the typical VMD workflow, you can see that the
combination of .psf with .pdb is
the most common way to have the complete system information and bonds
read in by VMD.

cheers,
     axel.

>
> Thank you.
> Elias
>
> -----------------------------------------------------------------------------------------
>
>
> HEADER
> ATOM 1 C BEA 6 49.668 21.668 21.668
> ATOM 2 C BEA 6 45.668 21.668 21.668
> ATOM 3 C BEA 6 41.668 21.668 21.668
> ATOM 4 C BEA 6 37.668 21.668 21.668
> ATOM 5 C BEA 6 33.668 21.668 21.668
> ATOM 6 C BEA 6 29.668 21.668 21.668
> CONECT 1 2
> CONECT 2 3
> CONECT 3 4
> CONECT 4 5
> CONECT 5 6
> END
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.