[gmx-users] superimposed structures

Mark Abraham Mark.Abraham at anu.edu.au
Tue Dec 22 11:06:04 CET 2009

leila karami wrote:
> Hi
>  I used commands trjconv and trjcat for fitting and obtaining of 
> superimposed structure between initial and final structure 

You're much more likely to get any feedback if you tell us your command 
lines. I've lost track of the number of times I've said this to you so 
far :-) How are you generating what (you think) is a superimposition of 
initial and final structures? trjconv and trjcat don't do that.

> 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.

If you're concatenating your .pdb file, then you've done it wrong.

Otherwise, you should just open the coordinate file that contains the 
superimposed structure.

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

If it's an unrealistic structure, it will have unrealistic guesses made 
by VMD about where bonds might be.


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