[gmx-users] superimposed structures

[leila karami]

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 structures were shown
but there is some exessive bonds.

I did following works but problem was not solved.

I don’t have non-standard molecules in my pdb files.

When I load the initial and final structures only into VMD before
superposition with trjconv, they display correctly.

I loaded topology file first and then the coordinates on top of that.

I added END record after the TER

I attached my pdb file containing superimposed structure.

I attached picture that vmd shows with name 1.bmp. I specify some of excess
bonds.

Please guide me.
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