Re: [AMBER] cpptraj Tutorial C1

From: Jason Swails <>
Date: Fri, 3 Oct 2014 14:50:06 -0400

On Oct 3, 2014, at 2:36 PM, George Tzotzos <> wrote:

> Following up on the earlier message, if I create an input file
> trajin
> rms ToFirst :1-13&!.H= first out rmsd1.agr mass
> and then run
> cpptraj trpzip2.ff10.mbondi.parm7
> rmsd1.agr is generated and xmgrace opens it without problems
> Is there an explanation for this

When cpptraj reads an input file, it runs all of the commands after it hits the end of the file.

If you are running cpptraj in interactive mode, then you have to explicitly tell cpptraj to run the calculations (either with the command “go” or “run”). My guess is that you quit before running any of the commands.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Oct 03 2014 - 12:00:03 PDT
Custom Search