Hi,
I am using MMPBSA.py for the first time and am getting errors:
---- snip ----
Traceback (most recent call last):
File "/raid5/amber11/bin/MMPBSA.py", line 1467, in ?
verbose)
File "/raid5/amber11/src/mmpbsa_py/utils.py", line 1492, in gboutput
bonddif[x] = bonddif[x] - bond[x]
IndexError: list index out of range
As I was looking through the code, it appears that the program is expecting
the number of frames in the complex mdout file to be the same as the number
of frames in the receptor and ligand mdout files. If the number of frames
in each of the mdout files is not the same, then one gets the IndexError
shown above. Is this correct? I can see that this is reasonable if one is
using a single trajectory of the complex to get all three mdout files. But
I am using separate trajectories for the complex, receptor, and ligand, and
each trajectory has a different number of frames. Is this why I am getting
this error? If so, is there a work-around, besides truncating the longer
trajectories to the size of the shortest trajectory? Thank you for your
help.
Sid
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Received on Fri Nov 11 2011 - 16:00:02 PST
