VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_rub.de)
Date: Tue Oct 23 2007 - 01:05:26 CDT

Hi Emilia,

if the inhibitor is in both structures, i.e. both both "molecules" consist of
the protein and inhibitor, you can use the RMSD plugins

"Extensions -> Analysis -> RMSD Calculator"

of vmd to align them.

You have just to select the inhibitor in the menu. You may wish to check:

http://www.ks.uiuc.edu/Research/vmd/current/ug/node186.html#SECTION001441200000000000000

If you must align trajectories, uou could use
"Extensions -> Analysis -> RMSD Trajectory Tool"

Eddi

> Hi, all
>
> I am studying two protein binding to the same inhibitor, and I want to do
> the superposition of the two complex according to the inhibitor. could
> anybody give me some suggestion? thanks in advance!
>
> Emilia
> +--------------------------------------------------------------------------
>---+
>
> | Emilia L. Wu (Ph.D. student)
> | | State Key Laboratory of Molecular Reaction Dynamics,
> | | Dalian Institute of Chemical Physics, |Tel:(86411)84379352
> | | Chinese Academy of Sciences
> | |Fax:(86411)84675584 | Dalian 116023, P.R.China
> | |Email:emiliawu_at_dicp.ac.cn |
>
> +--------------------------------------------------------------------------
>---+ 

-- 
--
=============================================================================
Eduard Schreiner                     e-mail: eduard.schreiner_at_theochem.rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-22121
Ruhr-Universitaet Bochum - NC 03/52         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                              http://www.theochem.rub.de
=============================================================================