Yes, this helped.
Thanks!
Aseel
-----Original Message-----
From: Nhai [mailto:nhai.qn.gmail.com]
Sent: Sunday, October 23, 2016 6:33 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] centering a molecule in a frame with command line
cpptraj
You can write a small bash or python script to write input for cpptraj and
then run it with
cpptraj -i file.in
Check -i option for further info.
Hai
> On Oct 23, 2016, at 6:25 PM, Aseel Bala Ahmed <balaahme.msu.edu> wrote:
>
> Hi,
> 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:
> cpptraj
>
> parm simbox.prmtop
> trajin frame3302.inpcrd
> center :3 origin
> image origin center familiar
> trajout frame3302cen3.inpcrd restart
> go
> 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?
>
> Thanks!
> Regards,
>
> Aseel Bala
>
> Chemical Engineering PhD Student
> Michigan State University
>
>
>
>
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Received on Sun Oct 23 2016 - 18:30:04 PDT
