Dear JasonMany thanks for the email, I was keep going with the tutorial but the file rmsd1.agr did not produce after I run the following command in the tutorial:
rms ToFirst :1-13&!.H= first out rmsd1.agr mass
[maryam.cluster ~]$cpptraj
CPPTRAJ: TrajectoryAnalysis. V1.0.5
INPUT: Reading Inputfrom STDIN, type "go" to run, "quit" to exit:
> parmtrpzip2.ff10.mbondi.parm7
[parm trpzip2.ff10.mbondi.parm7]
> trajintrpzip2.gb.nc
[trajin trpzip2.gb.nc]
> rms ToFirst:1-13&!.H= first out rmsd1.agr mass
[rms ToFirst :1-13&!.H= first outrmsd1.agr mass]
Thanks in advance for your help.
CheersMaryam
On Saturday, 28 February 2015, 14:43, Jason Swails <jason.swails.gmail.com> wrote:
On Sat, Feb 28, 2015 at 2:14 AM, Maryam Hamzehee <maryam_h_7860.yahoo.com>
wrote:
> Dear Amber list
> I am trying to run the tutorial C1 (
> http://ambermd.org/tutorials/analysis/tutorial1/), I ran the cpptraj and
> followed the tutorial C1, I was expecting to see the messages in tutorial
> (i.e. > parm trpzip2.ff10.mbondi.parm7 Reading 'trpzip2.ff10.mbondi.parm7'
> as Amber Topology> trajin trpzip2.gb.nc Reading 'trpzip2.gb.nc' as
> Amber NetCDF)
> but the following messages were observed:
> [maryam.cluster ~]$ 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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Received on Sat Feb 28 2015 - 04:30:02 PST
