[AMBER] Error in the apr.py code - steered MD simulation

From: Eduardo R. Almeida <eduardoe.r.a.hotmail.com>
Date: Tue, 5 Jan 2021 03:29:23 +0000

Dear Amber users,

I have been trying to perform umbrella sampling simulations of a host-guest system involving a cisplatin molecule encapsulated into a carbon nanotube structure. My ideia is to derive the potential of mean force (and the energy barrier) referring to the release of this Pt(II) drug from the cavity of the carbon nanostructure.In order to do this task, I have been reading the Amber tutorial: Computing Binding Free Energy using the Attach-Pull-Release (APR) Method. However, I got some errors when I tried to run the apr.py code:


eduardo.inspiron5480:~/Documents/Projeto_Doutorado/cddp_CNH/3cddp_CNHox/US/APR$ python2.7 apr.py eq -i apr.in<http://apr.in/> -s continue
 Welcome to APR: a tool for binding calculations. Version 1.1
 Written by:
   Niel M. Henriksen, Jian (Jane) Yin, David R. Slochower
 and the project leader:
   Michael K. Gilson
 Copyright (c) 2016-2017, University of California, San Diego
The current APR scripts may not be directly applied to protein systems, especially
for those with buried binding sites. Careful adjustments of the protocols and scripts
will be needed, based on the requirements of every particular system.

Checking the version of Python installed ...
You are using Python 2.7, which is perfect for running the APR scripts.

Setting up the APR framework ...
Continue mode enabled. Checking previous simulations ...
pmemd.cuda is on.
Translational and rotational restraints will be imposed.
No conformational restraints applied.
Hydrogen mass repartitioning (HMR) is on.

You can use Ctrl+C to quit the program.

Preparing folder windows/a00 2021-01-04 11:06:25 PM
Traceback (most recent call last):
  File "apr.py", line 1190, in <module>
  File "apr.py", line 1165, in main
  File "apr.py", line 906, in run_setup
  File "apr.py", line 433, in prepare_and_simulate
    shutil.copyfile('align_z.pdb', 'vac.pdb')
  File "/usr/lib/python2.7/shutil.py", line 96, in copyfile
    with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: 'align_z.pdb'
eduardo.inspiron5480:~/Documents/Projeto_Doutorado/cddp_CNH/3cddp_CNHox/US/APR$ ls


Firstly, could someone help me with this error?

I would like to ask you if it is possible to build the inputs of this simulation (steered molecular dynamics simulations and umbrella sampling simulations) in a conventional way without using the codes in python. If possible, could you help me to build an input file as an example? Another alternative would be to fix the error in the apr.py. However, since I am a beginner in this field (programming), I really do not know how to fix this error in the apr.py.



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Received on Mon Jan 04 2021 - 19:30:02 PST
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