AMBER Archive (2003)

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

From: Teletchéa Stéphane (steletch_at_biomedicale.univ-paris5.fr)
Date: Thu Nov 13 2003 - 16:46:48 CST

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 : http://www.steletch.org/article.php3?id_article=10

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.

Good.

> You could try updating to the new ptraj sources at
>
> http://www.chpc.utah.edu/~cheatham/software.html
>
> 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. 

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