From: Ashar Malik (
Date: Sun Jul 22 2018 - 05:48:29 CDT

Your message isn't clear - but will try to answer it.

Two things ---

one reason for the same frame being written out is that you are probably
not "updating" your selection. You need to update selection when you
iterate over your trajectory. (I assume this is what you meant when you
were referring to "same PDB for all frames")

On the other end, you want to write 2 molecules superimposed into a PDB.
That can't be done.

You need additional processing --

e.g. you can save the superimposed molecules as merged PDBs -- which means
that the two structures will be separated by a "ter" record.

then when you load the molecules, they will be loaded as separate frames --
and you can do some manipulation then and view both simultaneously.
Alternatively, what you may do is to superimpose the two proteins -- so one
will have moved to fit over the other and save the moved structure. NOw you
have 2 PDBs -- and you can load them simultaneously and you won't have to
do the aligning part again.

Either-way, if I understood you correctly, what you are trying to do
doesn't have a straightforward way (at least in my experience).

Feel free to write back if something is unclear.

On Sun, Jul 22, 2018 at 6:32 PM <> wrote:

> Hi All
> I have molecular dynamic simulation data of ubiquitin protein. I want to
> superimpose two frame and want to generate pdb of the superimposed frame.
> I have tried to manipulate on the aligning section of the vmd script of
> finding 'align and average structure'. But all time script is generating
> same pdb for all frame number.
> If you have any idea please let me know.
> Thanking you.
> Regards
> Abhik