AMBER Archive (2007)

Subject: Re: AMBER: radius of gyration

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Mon Jan 29 2007 - 16:27:34 CST

Thank you very much for your reply.
  I have another one question:
   
  I want to calcuate the distance between the specified atom to
the center of the mass of the molecue, Ptraj of Amber 8 can do that? I found Carnal can do it, I am just wondering whether Ptraj (Amber8) can do it. I checked it, it seems not. Is it right? If yes, know how to do it with Ptraj (Amber8).
  Thanks for your help!
  Bests,
  

 
  

Thomas Cheatham III <tec3_at_utah.edu> wrote:
  
> Sorry, could you please tell me some details for the download of Praj? I
> tried to find it on the website, but I didn't.

There is a link on the AMBER WWW page that points to my out-dated (2003)
ptraj version (www.chpc.utah.edu/~cheatham/software.html). However, that
version is not up-to-date with AMBER 9.0 and does not implement the radius
of gyration. Soon I'll update my WWW page and the AMBER page to release a
stand-alone version that has the full capabilities of ptraj in AMBER 9.0;
until then, your only choice for radius of gyration is working through
carnal, AMBER 9.0, or by cribbing some code/program off the net...

-- tec3 @ utah.edu

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Esther B.

 
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