AMBER Archive (2003)

Subject: Re: AMBER: regarding trajectory input and output with ptraj or Carnal

From: David Case (case_at_scripps.edu)
Date: Thu Oct 02 2003 - 07:54:11 CDT

On Thu, Oct 02, 2003, Vlad Cojocaru wrote:

> I have several dcd trajectories from NAMD. First question is: Does
> Carnal support dcd input? If not I would like to transform them into
> amber trajectories using ptraj, but I would like to do it in such a way
> (like in Carnal) to select each 10th frame and to output the trajectory
> after rms fitting to the first frame. I couldnt find in the amber manual
> such an option for ptraj. Could somebody guide me just a bit into this?

see the "trajin" command in ptraj to choose every 10th frame. See the
"rms" option to do rms fitting to the first frame.

....good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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