[gmx-users] About Mike Harms python script

[Justin A. Lemkul]

On 6/16/12 11:49 AM, vidhya sankar wrote:
> 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

Based on the error message, it would seem that your dist.xvg file doesn't have 
anything in it.  What does it contain?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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