VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jun 29 2007 - 12:48:33 CDT

Hi Charlotte,
out of curiosity, how did you generate the membrane around the protein?
The easiest way to do this is with the membrane plugin; if you did it
that way, you should already have a pdb and psf of the membrane embedded
protein.

In general, if you want to move and save things together in VMD, it's
best to make them part of same molecule. If you have pdb files of the
two separate molecules, you can just concatenate them in a text editor
and remove all END tags except for the one at the very end of the file.

Please let me know if this doesn't clear things up.

Best,
Peter

Charlotte J Siska wrote:
> I am trying right now to make a simulation of the electron transport chain, and right now I am at complex II. I am at the stage where I need to save a format on vmd of the protein in the membrane. I have tried to save the state, but when I open it again the membrane is missing and I have only the protein. I tried saving the coordinates but all I got was a very long line, making me think I somehow made my protein linear.
>
> Is there another way that I can save the protein embedded in the membrane? Or is it impossible?
>
> Also: I am having trouble moving the protein and membrane around when I have them both open in vmd at the same time. Is there a way where I can set a coordinate system to make this a little easier? Thanks!
>