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

From: David Case <>
Date: Thu, 2 Oct 2003 05:54:11 -0700

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

David A. Case                     |  e-mail:
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            |
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Received on Thu Oct 02 2003 - 14:53:01 PDT
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