Dear Vidhyh Sankar,
>IndexError: list index out of range
When a program reads in lists or arrays, in the software there is usually a set
size, for lines or number of atoms, etc... If the array or list is longer than
the set value you get this error. Also, if a counter is off, ie stops one
short through an iteration usually from not reading lines properly or geting a
returned length for an index which has changed in length...
It either means one of the following:
2 of your files dont match in size (ie number of atoms)
1 of your files has the formatting wrong, ie lines are speced too long, so it
doesnt read them properly
or theres a problem with the script, where it gets incorrect index lenghts.
if you look at the lines mentioned in the setupUmbrella.py script, it will tell
you exactly what it is trying to read in, and you can then either know if its
missmatch, or your files are formatted wrong.
Id wait and see, somone might be able to tell you off the bat exactly what the
error is though. In my experience, it can often be a secound carriage return
or space at the end of a .gro, or .dat or .sh file.
Stephan Watkins
-------- Original-Nachricht --------
> Datum: Sat, 16 Jun 2012 23:49:06 +0800 (SGT)
> Von: vidhya sankar <scvsankar_...@yahoo.com>
> An: "gmx-users@gromacs.org" <gmx-users@gromacs.org>
> Betreff: [gmx-users] About Mike Harms python script
> Dear justin Thank you for your previous reply
>
> I am doing Umbrella sampling in
> gromacs
>
> I have 30 set of initial configuration in .gro file format .Now i would
> like to do NPT equilibration and umbrella sampling for all these
> configuration (for these i have to carry out 30 times equilibration and 30
> times
> umbrella sampling) to Automate these process i used the python script
> provided by Mike Harms. but when invoke the command as follows
> ./setupUmbrella.py summary_distances.dat 0.2 run-umbrella.sh &>
> caught-output.txt
> I got error as follows in Caught_output .txt
>
>
> Traceback (most recent call last):
> File "./setupUmbrella.py", line 182, in <module>
> out = main()
> File "./setupUmbrella.py", line 150, in main
> distance_table = readDistanceFile(distance_file)
> File "./setupUmbrella.py", line 49, in readDistanceFile
> value = float(columns[1])
> IndexError: list index out of range
>
> I have all the required files ( index.ndx files , dist.xvg files, , .gro
> files and .mdp files) in the running directory
>
> How to solve these error
> Thanks In advance
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