VMD-L Mailing List

From: Luca Bellucci (bellucci14_at_unisi.it)
Date: Sat Dec 19 2009 - 16:06:12 CST

Hi Balazs,
you can try with the following commands:
pbc wrap -centersel protein -center com -compound res
to rebuild water cell around the protein you can tray also with the following command:
pbc wrap -center bb -centersel protein -sel "not protein " -compound res

> Dear All,
> I performed MD simulation of a membrane protein in membrane environment.
> My protein moves from the periodic box (which is normal I know), and I
> would like to wrap it in the unit cell, and to set the unit cell center
> on the protein com.
> I used the following commands:
> set center [atomselect top protein]
> pbc wrap -centersel $center -center com -compound res
>
> and I obtained the following error message:
> atomselect: cannot parse selection text: (atomselect42)
>
> I made a mistake in the commands, or there is other issue?
> How can I make the wrapping?
> Any help will be appreciated!
> Thanks!
> Balazs
>
>