Re: [AMBER] Trajectory processing using ptraj

From: Daniel Roe <>
Date: Tue, 20 Jan 2015 11:27:55 -0700


You're using cpptraj syntax in a lot of these commands. You need to
use cpptraj instead of ptraj for this script to work.

On Tue, Jan 20, 2015 at 10:53 AM, James Starlight
<> wrote:
> trajin 0 last 1

The 'last' keyword for 'trajin' is cpptraj-only. There is no
equivalent in ptraj. However, since your offset is '1' you can just
use ' trajin' and all frames will be read.

> # fitting to protein
> center :1-361 mass origin
> image origin center

For most cases, 'autoimage' is the recommended command for imaging
instead of 'center'/'image' (again, cpptraj only).

> trajout md_proc.dcd dcd nobox

The 'dcd' keyword is cpptraj-only. For DCD output with ptraj, only the
'charmm' keyword works. If you look at your output it likely says it's
defaulting to Amber trajectory format here.

My recommendation is to just use cpptraj (from AmberTools 14) since
ptraj is no longer actively developed.


> ! in fact
> 1) it produce again full system trajectory without stripping the solvent
> 2) broken dcd file (is not recognized by VMD) but there is no problem if I
> chose netCDF output again
> Thanks for help,
> James
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jan 20 2015 - 10:30:04 PST
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