I guess I wasn't clear enough ....
1) ptraj and cpptraj are DIFFERENT programs! cpptraj enhances
many of the features of ptraj and can be used identically to ptraj
for nearly all ptraj commands, but it is a separate program.
2) The autoimage command is only available for AmberTools 12 with
bugfixes. Also, autoimage is only available for cpptraj.
3) Are you able to install AmberTools 12 at your location? (it's free.)
If not, then your problem becomes a little more challenging and you'll
need to send us some test files to determine the appropriate imaging
commands.
--Niel
________________________________________
From: Sindrila Dutta banik [sindrila.duttabanik.yahoo.com]
Sent: Sunday, November 04, 2012 8:57 PM
To: AMBER Mailing List
Subject: [AMBER] Problem related to RMSD
I use amber11. I modify the script file of ptraj accordingly but it shows the following error:
WARNING in dispatchToken: Token string "autoimage" not found in tokenlist
Is 'autoimage' compatible with only Amber12? How to do this in Amber11? I go through the amber11 manual. 'image' command is available there, but not autoimage.
With best regards
Sindrila
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 5 November 2012 7:05 AM
Subject: Re: [AMBER] Problem related to RMSD
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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 20:30:03 PST
