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
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