Hi Jason. Thank you for the update. When you said that is going to be quite
slow, did you mean that it would take days. Cause I've been running it for
about 4 hours and the
Re-ordering the trajectories. This may take awhile...
Adding mdcrd.md2: 0%
Is still at 0%. The system has less than 30k atoms and the simulation has
10k frames.
Is this what I should expect?
Thanks
2013/7/11 Jason Swails <jason.swails.gmail.com>
> On Thu, Jul 11, 2013 at 7:04 PM, Fabrício Bracht <fabracht1.gmail.com
> >wrote:
>
> > Hi Jason. Indeed my input had a silly mistake. Instead of using -x to
> > indicate the output trajectory, I used -y again. Very silly indeed.
> > Now I have another error.
> > The input line
> > ./fix_traj_parm.py -p HOH_wat.prmtop -y mdcrd.md2 mdcrd.md3 -o
> > fixedparm.prmtop -x fixed.mdcrd
> > seems to be correct, but an error comes up anyway:
> >
> > Re-ordering the trajectories. This may take awhile...
> > Traceback (most recent call last):
> > File "./fix_traj_parm.py", line 110, in <module>
> > pbcang =
> > newtraj.createVariable('cell_angular','d',('frame','cell_angular'))
> > IOError: netcdf: NetCDF: String match to name in use
> >
>
> Ah, a stupid typo (in 2 places, actually).
>
> When I tested this script, I created an system without PBC, so I never
> tested this particular bit of code... It seems to work now, although it
> may be quite slow for large systems (it is in Python, after all).
>
> I've uploaded the fixed version to my Wiki.
>
> Thanks,
> Jason
>
>
> > I have tried with two different sets of trajectories and the error was
> the
> > same.
> >
> >
> >
> > 2013/7/11 Jason Swails <jason.swails.gmail.com>
> >
> > > On Thu, Jul 11, 2013 at 1:30 PM, Fabrício Bracht <fabracht1.gmail.com
> > > >wrote:
> > >
> > > > Hi Jason. Thanks for the reply. It worked fine until it started
> working
> > > on
> > > > the trajectory. Here is the screen output:
> > > >
> > > > Re-ordering the trajectories. This may take awhile...
> > > > Traceback (most recent call last):
> > > > File "./fix_traj_parm.py", line 70, in <module>
> > > > newtraj = open_netcdf(opt.outtraj, 'w')
> > > > File "/home/fabricio/amber12/bin/chemistry/amber/readparm.py", line
> > 45,
> > > > in <lambda>
> > > > open_netcdf = lambda name, mode: NetCDFFile(name, mode)
> > > > File "/usr/lib/python2.7/dist-packages/Scientific/IO/NetCDF.py",
> line
> > > > 171, in NetCDFFile
> > > > filename = os.path.expanduser(filename)
> > > > File "/usr/lib/python2.7/posixpath.py", line 252, in expanduser
> > > > if not path.startswith('~'):
> > > > AttributeError: 'NoneType' object has no attribute 'startswith'
> > > >
> > > > Looked it up on the web to see if there was something I could do, but
> > > found
> > > > lots of generic forums discussing things that I didn't really
> > understand.
> > > >
> > > > Am I missing something here?
> > > >
> > >
> > > Could be. What command-line did you use (user input is frequently
> > helpful
> > > debugging information)? It *looks* like you didn't specify an output
> > > trajectory on the command-line, so the default "None" (Python
> equivalent
> > of
> > > NULL) was passed to the NetCDF constructor. Apparently I did not add
> > much
> > > error checking to make sure that the user input was sufficient. You
> can
> > > use the "--help" flag to provide some level of help.
> > >
> > > Note, this script does _not_ modify the trajectories in-place. It
> > writes a
> > > new trajectory that is a concatenation of all input trajectories (and
> so
> > > requires you to supply an output trajectory).
> > >
> > > This script is intended to be used *once* for your system. That is, if
> > you
> > > ran your simulation in 20 chunks, you should supply your prmtop file
> and
> > 20
> > > NetCDF trajectories, after which fix_parm_traj.py will create one new,
> > > fixed prmtop and ONE, concatenated, properly ordered NetCDF trajectory.
> > >
> > > Hope this helps,
> > > Jason
> > >
> > > P.S. While 99.9% of my Python scripts have a sophisticated command-line
> > > parser that documents all options with the "--help" flag, mature input
> > > error-checking I tend to reserve for scripts and programs I release for
> > > general use (e.g., MMPBSA.py, ParmEd, cpinutil.py, update_amber, etc.)
> > >
> > > --
> > >
> > >
> > > Ja
> > >
> > > son M. Swails
> > > Qu
> > >
> > >
> > > antum Theory Project,
> > > Un
> > >
> > > iversity of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jul 11 2013 - 20:30:04 PDT
