[AMBER] MAWS/Amber and python program adjustment

From: Bruno Cramer <bruno.cramer.gmail.com>
Date: Tue, 27 Aug 2019 19:53:53 -0300

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 =

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

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


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Received on Tue Aug 27 2019 - 16:00:02 PDT
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