[gmx-users] superimposition

[Mark Abraham]

leila karami wrote:
> Hi
>  
> I used commands trjconv and trjcat for fitting and obtaining of 
> superimposed structure between initial and final structure but when I 
> open pdb file containing superimposed structure with VMD, 2 structure 
> were shown but there is some exessive bonds.

I'm not sure about your use of "superimposed" here.

http://www.gromacs.org/Documentation/Terminology/Average_Structure

or

http://www.gromacs.org/About_Gromacs/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds

probably answer your issue.

If you've somehow edited your file or forced VMD to read the two 
structures as one, then of course there will be excess bonds.

Mark