Hello MS users,

I have generated a trajectory file for several conformations of my molecule. The numbering/naming of the atoms (C-1, C-2, C-3…) is made visible by using a perl script. When I extract the coordinate file (XYZ) from the .xtd file, it writes the coordinates in the same order (C-1 at the first line, C-2 at the second line and so on). What I want is to exchange the numbering of the symmetric atoms (like N-34 by N-35 and vise versa). In order to do this, In my .xsd structure, I have used the “Properties Explorer” to rename N-34 as N-35 and N-35 as N-34 and same for other atoms. Now the .xsd structure and the .xtd trajectories show the updated numbering/naming of all the atoms. But when I extract the coordinates from the .xtd file, it writes the coordinates according to the old assignment. According to the new assignment the C-1 is replaced by C-29 and C-29 by C-1, so it should write the coordinates of C-29 (now which is C-1) at the first line. But it writes as per the old assignment. I can’t find the way to solve this. I wish somebody can help me on this.

I have attached my structure image and the perl script I am using to extract he coordinates.

Thanks

Anant