[gmx-users] superimposition

Mark Abraham Mark.Abraham at anu.edu.au
Mon Dec 14 09:40:43 CET 2009

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.




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.


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