Re: [AMBER] cpptraj, ptraj and time interval

From: Liu Denis <>
Date: Fri, 20 Apr 2012 08:38:39 +0800

Hi Fabricio:
    Cpptraj is well documented in AmberTools 12 manual. The syntax of
trajin in cpptrj is similar to the one in ptraj.
  Please refer to Page 171, I copied it here:

trajin <filename> [<start> [[<stop> | last] [<offset>]]] | lastframe
[parm <parmfile> | parmindex <#>]
[remdtraj remdtrajtemp <Temperature> remdout <outprefix> [netcdf]
trajnames <Comma-separated name list>]

Read in trajectory specified by filename. Currently Cpptraj will recognize
Amber trajectories,
Amber Netcdf Trajectories, Charmm DCD trajectories, Amber Restart files,
PDB files, and
TRIPOS MOL2 files. The frames to be read in can be specified with the
<start>, <stop>, and
<offset> arguments (defaults are first frame, last frame, and 1
respectively). If just the <start>
argument is given, all frames from <start> to the last frame of the
trjaectory will be read. To
read in a trajectory with offsets where the last frame # is not known,
specify thelast keyword
instead of a <stop> argument, e.g.

trajin Test1.crd 10 last 2

This will process Test1.crd from frame 10 to the last frame, skipping by 2
frames. To explicitly
select only the last frame, specify thelastframe keyword:

trajin Test1.crd lastframe

2012/4/20 Fabrício Bracht <>

> Is there a way to define the time interval using cpptraj. In ptraj all
> you have to do is define " time <time interval> " in the config file,
> but I haven't found any mention about this with cpptraj.
> Thank you
> Fabrício Bracht
> _______________________________________________
> AMBER mailing list

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Received on Thu Apr 19 2012 - 18:30:04 PDT
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