Re: [AMBER] cpptraj, ptraj and time interval

From: Fabrício Bracht <>
Date: Fri, 20 Apr 2012 11:25:52 -0300

Hi Liu. I read the documentation on cpptraj. The problem is that the
{offset} mask is not exactly what I need. The thing is: my trajectory
was written every 2ps. When cpptraj reads the trajectory (for
instance, while doing secstruct) it writes a file that has on the x
axis the number of frames and not the amount of ps that were
simulated. For example, if I simulate 10000 ps saving every 2ps,
cpptraj will write a graph from 0 to 5000. In this case, I actually
have all 5000 frames on the graph, but it does not correspond to my
simulation time. The offset mask will simply skip frames, not
analysing them at all. With ptraj, when I specify the 'time' variable,
it understands that my simulation was written every 2 ps. So in this
case, does it mean that I will have to write a script to change the
frame values to match my simulation time?
Was this too confusing? I don't know if I was clear enough. Please let
me know if I'm being too confusing.
Thank you

2012/4/19 Liu Denis <>:
> 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 Fri Apr 20 2012 - 07:30:07 PDT
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