From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Fri Mar 29 2013 - 08:47:33 CDT
Try "pbc wrap -all -orthorhombic -compound fragment -center com -centersel
protein" in VMD or something equivalent.
Thomas
On 29 March 2013 00:44, Maria Bykhovskaia <mb.ucdelcaribe_at_gmail.com> wrote:
> I need to measure the distance between the protein and ions after
> prolonged MD. However, a part of the protein crossed the border of the cell
> (not wrapped around). I need to find out how close are certain ions to
> certain groups of the protein, but these protein groups moved out of the
> cell. Is there a way to recenter the water box with ions around the protein?
> Thank you,
> Maria
>
> --
> Maria Bykhovskaia
> Professor and Chair
> Neuroscience Department
> Universidad Central del Caribe
> Bayamon, Puerto Rico
> http://maria.ucdelcaribe.org
> http://neuro.ucdelcaribe.org
>
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:06 CST