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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
Esther B.
---------------------------------
Need Mail bonding?
Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
|