Dear MAWS/Amber and python user
I am very interested in using MAWS Here is a partial solution of my last
thread but I still get errors from python.
I could solve the problems for the files ['DGN', 'DAN', 'DTN', 'DCN'].
Here is what I did using Amber/AmberTools v.19 and following the
recommendation from Gerald Monard to whom I thank.
1- Replace the force field: Line 25 of MAWS.py 'force field_name =
"leaprc.DNA.bsc1"
2- Do the same replacement in lines 1076, 1153, 1311
3- run MAWS: python3 MAWS_rev1.py -b 0.01 -i 200 -s 200 -l 15 -t 0.01 -f
mol2 -y HYBRID PATH INFILE
This will generate the required files DGN', 'DAN', 'DTN', 'DCN each with
prefix respectively, "prmtop" and "inpcdr" .
But I still get error from python code and I don't know how to solve it as
I am not a python expert. The source code is not giving me a clue
Traceback (most recent call last):
File "/home/bcramer/miniconda3/lib/python3.7/multiprocessing/pool.py",
line 121, in worker
result = (True, func(*args, **kwds))
File "/home/bcramer/miniconda3/lib/python3.7/multiprocessing/pool.py",
line 44, in mapstar
return list(map(*args))
File "MAWS_rev1.py", line 1090, in initial
ligand_range = get_ligand_range(aptamer_top.topology)
File "MAWS_rev1.py", line 197, in get_ligand_range
return [get_ligand(topology)[0], len(get_ligand(topology))]
*IndexError: list index out of range*
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "MAWS_rev1.py", line 1357, in <module>
positions_and_Ntides = loop()
File "MAWS_rev1.py", line 1237, in loop
pos_Nt_S_task = pool.map(initial, alphabet)
File "/home/bcramer/miniconda3/lib/python3.7/multiprocessing/pool.py",
line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/bcramer/miniconda3/lib/python3.7/multiprocessing/pool.py",
line 657, in get
raise self._value
IndexError: list index out of range
Attached the source code with updated force field.
Thank you
Bruno
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Received on Tue Aug 27 2019 - 16:00:02 PDT
