[gmx-users] About Mike Harms python script

vidhya sankar scvsankar_agr at yahoo.com
Sat Jun 16 17:49:06 CEST 2012

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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