Thanks for the reply.
By the way, I have tried reinstall python-scientific. Then tried to run the script nctorst.py. In the script I changed " frame = 200" and "inputfile = 'waters1445-MD010-run1000.traj' " . Because each traj file contains 200 frames.
When I run the script typing python nctorst.py, I get error message as below
vijay.glycosim:~/Simulation-Folder-oct2012/water-only/Production-waters1445$ python nctorst.py
title 200
Traceback (most recent call last):
File "nctorst.py", line 31, in <module>
print "%5i%15.7e" % (shape[1],ncfile.variables['time'][frame])
IOError: Index exceeds dimension bound
vijay.glycosim:~/Simulation-Folder-oct2012/water-only/Production-waters1445$
I am little bit lost here. Is this script need any other input?
Appreciate any help.
Regards
Vijay
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: Vijay Manickam Achari <vjrajamany.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, 13 December 2012, 20:54
Subject: Re: [AMBER] extract velocity from traj files
On Thu, Dec 13, 2012 at 4:08 AM, Vijay Manickam Achari <vjrajamany.yahoo.com
> wrote:
> I would like to extract velocity from trajectory files.
> I have used ntwv = -1 and ioutfm = 1 in the input parameter file.
>
> According to AMBER mailing list (
> http://archive.ambermd.org/201011/0255.html), I installed
> python-scientific in Ubuntu-11.10
> and tried to execute the script. But It failed to run.
>
> The output is as below:
>
> [vijay.glycogpu extract-vel]$ python extractvel.py
> Traceback (most recent call last):
> File "extractvel.py", line 1, in <module>
> from Scientific.IO.NetCDF import NetCDFFile as Dataset
> ImportError: No module named Scientific.IO.NetCDF
> [vijay.glycogpu extract-vel]$
>
>
> Is there anything additional things need to be done?
> Please advice.
>
On my Ubuntu system (12.04), after installing python-scientific,
Scientific.IO.NetCDF.NetCDFFile could be imported without any problems (and
the likelihood that 11.10 is broken in this regard is very low). My guess
is one of two things happened: you have another (non-system) python (type
'which python' to make sure that it returns /usr/bin/python) that is being
invoked by default -- this 'other' python would not have the Scientific
package. Or, python-scientific did not install properly. Note the
difference between scipy and ScientificPython -- they are distinct packages
that do different things.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Dec 13 2012 - 21:30:02 PST
