[AMBER] centering a molecule in a frame with command line cpptraj

From: Aseel Bala Ahmed <balaahme.msu.edu>
Date: Sun, 23 Oct 2016 18:25:15 -0400

I would like to center a molecule in a box and generate the inpcrd for the
frame. I am able to do that well using cpptraj by doing the following:
        parm simbox.prmtop
        trajin frame3302.inpcrd
        center :3 origin
        image origin center familiar
        trajout frame3302cen3.inpcrd restart

I put in the 'restart' at the end of the trajout line so that the file is
formatted correctly to be subsequently used as an input to sander.

Now, I am finding that I need to do all the cpptraj work through command
line using flags.
The AMBER documentation only shows the flags for the input file and output
file but not for the formatting of the output file or other operations (such
as center here). I tried to do the following:

        cpptraj -p simbox.prmtop center :2 origin image origin center
familiar -y frame3302.inpcrd -x f3302c.inpcrd restart

and also

        cpptraj -p simbox.prmtop -y frame3302.inpcrd center :2 origin image
origin center familiar -x f3302c.inpcrd restart

but I keep getting the error:
        Unrecognized input on command line

And I think it's because I don't have the correct flags. Can someone help me
put all of this on one command line with the correct flags?


Aseel Bala

Chemical Engineering PhD Student
Michigan State University

AMBER mailing list
Received on Sun Oct 23 2016 - 15:30:02 PDT
Custom Search