AMBER Archive (2004)

Subject: Re: AMBER: An question about PTRAJ

From: Stef (steletch_at_free.fr)
Date: Sat Sep 11 2004 - 03:01:52 CDT

Le samedi 11 septembre 2004 à 09:29 +0800, b86203054_at_ntu.edu.tw a
écrit :
> Dear sir
> My name is Morris. I wet a problem when I was using the IMAGE function
> of the PTRAJ.
> Due to the periodic box condition, my DNA and its bindtion protein were
> seperated visually. For my analysis, I tried to used the PTRAJ to put them
> together. According the instruction, I use the IMAGE. But I can't solve the
> problem.
> The commands which I had used are listed bleow:
> 1, image origin, I got single strand back. The other one is still in the other
> side of the box.
> 2, image center bymask :195-218, no function.
> 3, image center:195-218 bymask :195-218, still no function
> the 195-218 is the residue number of DNA double helix
>
> If you have similiar experience, please let me know your solution. I'll
> appreciate it.
> Sincerely
>
> Y. Morris Chen

Have a look at :
http://www.steletch.org/article.php3?id_article=10

I solved a similar problem there ;-)

Stef 

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