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
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
> _______________________________________________
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>
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Received on Thu Jul 11 2013 - 16:30:02 PDT
