[gmx-users] superimposed structures
karami.leila1 at gmail.com
Tue Dec 22 09:52:53 CET 2009
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
Please guide me.
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