Just a minor comment to Niel's email (which is correct). Cpptraj was
designed to be completely compatible with ptraj, so you can use it exactly
the same way. In your script, use "autoimage" instead of your center and
image commands, and just use cpptraj instead of ptraj for the executable.
I second the suggestion about reading the manual, too.
Good luck,
Jason
On Sun, Nov 4, 2012 at 12:57 PM, Niel Henriksen <niel.henriksen.utah.edu>wrote:
> You need to use AmberTools 12 with at least bugfix 16.
>
> cpptraj is a separate, although similar program to ptraj.
> Read the manual to learn more about it.
>
> You should make a command file that uses a sequence
> similar to the following:
>
> parm <prmtop file>
> trajin <mdcrd file>
> autoimage
> rmsd <rmsd commands>
>
> Then you can execute: cpptraj -i command.file
>
> Unless you have a complicated solute system, you should
> get the correct results.
>
> --Niel
> ________________________________________
> From: Sindrila Dutta banik [sindrila.duttabanik.yahoo.com]
> Sent: Sunday, November 04, 2012 10:43 AM
> To: AMBER Mailing List
> Subject: [AMBER] Problem related to RMSD
>
> How to use "autoimage command in cpptraj"
>
> I modify the script as follows:
>
> center :1-794 mass origin
> image origin center
>
> But the result is same. How to rectify this?
>
> Sindrila
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>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Nov 04 2012 - 18:00:03 PST
