VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jun 29 2007 - 15:31:51 CDT

Hi Charlotte,
sorry, mental mistake on my part -- I forgot that unlike (say) solvate,
membrane doesn't yet automatically embed the protein. What you'll need
to do is use VMD text commands to move the lipid patch to an appropriate
place, and then save the lipids that are not touching the protein. For
example, you can move the patch by making an atomselection and using the
moveby command:

set sel [atomselect top all]
$sel moveby {10 0 0}

to translate the whole patch 10 A along the x axis.

The steps to follow in order to get the protein properly embedded once
you've moved the patch to a position around the protein are identical to
those in the gramacidin tutorial
(http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/):

package require psfgen

# Read in structure files
readpsf protein.psf
readpsf lipids.psf

# Read in coordinates
coordpdb protein.pdb
coordpdb lipids.pdb

writepsf combined.psf
writepdb combined.pdb

(Assuming you have a psf/pdb file for your lipids and proteins).

Again, sorry for the confusion on my part.

Best,
Peter

Peter Freddolino wrote:
> 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!
>>
>>