Re: AMBER: Any correct way to image a molecule ?

From: Teletchéa Stéphane <>
Date: Thu, 13 Nov 2003 23:46:48 +0100

Le jeu 13/11/2003 à 22:58, Thomas E. Cheatham, III a écrit :
> > center origin
> > image center familiar
> I would use the commands below where :1-20 represents your DNA (assuming
> you had 20 bases):
> center :1-20 mass origin
> image origin center

I tried your solution, but without more luck. You can find a more
detailed report at :

The strange thing is that water molecules get imaged but not the counter
ions. May be it is coming from their name (CIP ?)

> Obviously you have to keep the ions and water for the imaging part
> (stripping or closestwaters can be done after the imaging).

I've tried also this option.

> The box coordinates use read in from the trajectory unless you overwrite
> them with the box command so I doubt this is the problem.


> You could try updating to the new ptraj sources at
> If this still leads to problems, we can try to resolve them...

I've downloaded them, i'll try tomorrow, it's getting late in France

Thanks a lot for your quick answer, i hope we'll find why the counter
ions are not well back in the box ...

If you have more hints ...

Stéphane T.
23:45:13 up 9:54, 9 users, load average: 0.02, 0.12, 0.20 
Linux 2.4.22-10stef.2mdkcustom #1 dim oct 26 23:59:10 CET 2003

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to

Received on Thu Nov 13 2003 - 22:53:01 PST
Custom Search