Hi,
On Sat, Feb 28, 2015 at 5:27 AM, Maryam Hamzehee
<maryam_h_7860.yahoo.com> wrote:
> [rms ToFirst :1-13&!.H= first outrmsd1.agr mass]
You need to make sure you are following all of the steps in the
tutorial. The next part of the tutorial mentions:
"Start the trajectory processing by typing 'run'."
You need to type 'run' or 'go' to make CPPTRAJ start processing
trajectories and whatever Actions you have set up.
More importantly, as Jason has previously indicated and as it states
at the beginning of the tutorial:
"Note: This tutorial was designed for use with CPPTRAJ from AmberTools 14."
I recommend always using the most up-to-date version of CPPTRAJ, which
is freely available as part of AmberTools 14:
http://ambermd.org/AmberTools14-get.html
Hope this helps,
-Dan
> Thanks in advance for your help.
> CheersMaryam
>
>
>
> On Saturday, 28 February 2015, 14:43, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> On Sat, Feb 28, 2015 at 2:14 AM, Maryam Hamzehee <maryam_h_7860.yahoo.com>
> wrote:
>
>> Dear Amber list
>> I am trying to run the tutorial C1 (
>> http://ambermd.org/tutorials/analysis/tutorial1/), I ran the cpptraj and
>> followed the tutorial C1, I was expecting to see the messages in tutorial
>> (i.e. > parm trpzip2.ff10.mbondi.parm7 Reading 'trpzip2.ff10.mbondi.parm7'
>> as Amber Topology> trajin trpzip2.gb.nc Reading 'trpzip2.gb.nc' as
>> Amber NetCDF)
>> but the following messages were observed:
>> [maryam.cluster ~]$ cpptraj
>> CPPTRAJ: Trajectory Analysis. V1.0.5 ___ ___ ___ ___ | \/ | \/ |
>> \/ | _|_/\_|_/\_|_/\_|_
>> INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:> parm
>> trpzip2.ff10.mbondi.parm7 [parm trpzip2.ff10.mbondi.parm7]> trajin
>> trpzip2.gb.nc [trajin trpzip2.gb.nc]
>>
>
> You are using version 1.0.5. If you look at the output from the tutorial,
> you will see that it corresponds to version 14.0.5 (the current version
> that I have is 14.22).
>
> You ned to upgrade to the latest version from AmberTools 14 to get the
> output to look the same.
>
> That said, this kind of output does occasionally change from version to
> version, so it is not always worrying when diagnostic information like this
> seems to change. It would be worrying if the results were drastically
> different. It is a challenge to keep tutorials up-to-date with the latest
> versions of all outputs.
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Feb 28 2015 - 07:00:02 PST
