VMD-L Mailing List

From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Fri Mar 30 2012 - 14:04:27 CDT

Your "PDB" format is not correct. It is very strict format and if you
get it wrong, you will get garbage. It's somewhat maddening because
even hidden tab characters will throw it off.

You can find the rules governing the PDB format here:
http://www.wwpdb.org/docs.html

It may be easiest to grab one of the PDB files from a NAMD tutorial and
use that as a template to build your file.
Regards,
J.

On 3/30/2012 12:37 PM, james Fernandez wrote:
> Hi VMD USERS,
> I am trying to plot some co-ordinates(points) on VMD and I
> used a simple format of a PDB file but its giving a wrong figure.
> The format of the pdb file that i used is as follows,
>
> 8!
> REMARK 350 BIOMOLECULE: 1
>
> ATOM 1 28.407 28.897 5.314 1.00 9.00
> ATOM 2 28.238 28.590 4.518 1.00 9.00
> ATOM 3 28.343 27.156 2.578 1.00 9.00
> ATOM 4 24.707 24.752 0.377 1.00 9.00
> ATOM 5 24.641 22.884 -1.74 1.00 9.00
> ATOM 6 23.405 19.850 -3.63 1.00 9.00
> ATOM 7 22.710 16.487 -4.12 1.00 9.00
> ATOM 8 22.205 13.628 -5.88 1.00 9.00
>
> I am trying to connect these molecules through bonds i am able to
> connect it but the co-ordinates that are getting plotted on VMD are
> not accurate.
>
> Can someone please help me in getting these co-ordinates plotted since
> I am NEW to this software. I will be very thankful to you and your
> help will be appreciated.
>
> Regards
> James 

-- 
=================================================================
Jeffrey J. Potoff			  jpotoff_at_wayne.edu
Associate Professor			  Wayne State University
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr			  Phone:(313)577-9357		
Detroit, MI 48202  	                  Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
=================================================================