It shows Warning...will it create some issue ?

[debanjansen48]

Hope installed it.. But returns following WARNING...

$:amber.python -m pip install gmx_MMPBSA
Collecting gmx_MMPBSA
Downloading gmx_MMPBSA-1.0.0-py3-none-any.whl (135 kB)
|████████████████████████████████| 135 kB 962 kB/s
Installing collected packages: gmx-MMPBSA
WARNING: The scripts gmx_MMPBSA and gmx_MMPBSA_gui are installed in '/home/debanjan/Amber/amber20/miniconda/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed gmx-MMPBSA-1.0.0

when I call it from the installed directory " '/home/debanjan/Amber/amber20/miniconda/bin" it returns following error
(base) debanjan@debanjan:/Amber/amber20/miniconda/bin$ gmx
gmx gmx_d gmx_MMPBSA gmx_MMPBSA_gui
(base) debanjan@debanjan:/Amber/amber20/miniconda/bin$ gmx_MMPBSA_gui
Traceback (most recent call last):
File "/home/debanjan/Amber/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 24, in
from GMXMMPBSA import main
File "/home/debanjan/Amber/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 44, in
from GMXMMPBSA.createinput import create_inputs
File "/home/debanjan/Amber/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/createinput.py", line 43, in
from parmed.amber.mdin import Mdin
ModuleNotFoundError: No module named 'parmed'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "./gmx_MMPBSA_gui", line 5, in
from GMXMMPBSA.app import gmxmmpbsa_gui
File "/home/debanjan/Amber/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 30, in
raise ImportError('Could not import Amber Python modules. Please make sure '
ImportError: Could not import Amber Python modules. Please make sure you have sourced /home/debanjan/Amber/amber20/amber.sh (if you are using sh/ksh/bash/zsh) or /home/debanjan/Amber/amber20/amber.csh (if you are using csh/tcsh)
(base) debanjan@debanjan:~/Amber/amber20/miniconda/bin$ gmx_MMPBSA
Traceback (most recent call last):
File "/home/debanjan/Amber/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 24, in
from GMXMMPBSA import main
File "/home/debanjan/Amber/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 44, in
from GMXMMPBSA.createinput import create_inputs
File "/home/debanjan/Amber/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/createinput.py", line 43, in
from parmed.amber.mdin import Mdin
ModuleNotFoundError: No module named 'parmed'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "./gmx_MMPBSA", line 5, in
from GMXMMPBSA.app import gmxmmpbsa
File "/home/debanjan/Amber/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 30, in
raise ImportError('Could not import Amber Python modules. Please make sure '
ImportError: Could not import Amber Python modules. Please make sure you have sourced /home/debanjan/Amber/amber20/amber.sh (if you are using sh/ksh/bash/zsh) or /home/debanjan/Amber/amber20/amber.csh (if you are using csh/tcsh)
(base) debanjan@debanjan:~/Amber/amber20/miniconda/bin$

However parmed is installed
(base) debanjan@debanjan:/Amber/amber20/miniconda/bin$ parm
parmcal parmchk2 parmed
(base) debanjan@debanjan:/Amber/amber20/miniconda/bin$ whereis parmed
parmed: /usr/local/bin/parmed /home/debanjan/Amber/amber20/bin/parmed

[Valdes-Tresanco-MS]

Please, check two things:

• Open the executable (/home/debanjan/Amber/amber20/miniconda/bin/gmx_MMPBSA) with a text editor and show me the content.
• run amber.python in a terminal and then show me the output when you enter the following line
  import parmed

[debanjansen48]

*Open the executable (/home/debanjan/Amber/amber20/**miniconda/bin/gmx_MMPBSA) with a text editor and show me the content.* #!/home/debanjan/Amber/amber20/bin/amber.python # -*- coding: utf-8 -*- import re import sys from GMXMMPBSA.app import gmxmmpbsa if __name__ == '__main__': sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) sys.exit(gmxmmpbsa()) *run amber.python in a terminal and then show me the output when you enter the following line* (base) debanjan@debanjan:~/Desktop$ amber.python Python 3.8.3 (default, May 19 2020, 18:47:26) [GCC 7.3.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information.

>> import parmed

Traceback (most recent call last): File "<stdin>", line 1, in <module> ModuleNotFoundError: No module named 'parmed'

…

On Tue, Nov 10, 2020 at 2:02 AM Mario Sergio Valdés Tresanco < ***@***.***> wrote: Please, check two things: - Open the executable (/home/debanjan/Amber/amber20/miniconda/bin/gmx_MMPBSA) with a text editor and show me the content. - run amber.python in a terminal and then show me the output when you enter the following line import parmed — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOJ7Q4UGISMO64WDHW73TUTSPBGW7ANCNFSM4TPSIC3A> .

[Valdes-Tresanco-MS]

Ok the problem is that amber.python does not detect the parmed module. This is probably because the python modules are not in the default path or the amber source has not been done correctly. Try adding this line to your .bashrc file
/home/debanjan/Amber/amber20/amber.sh

[debanjansen48]

I added that line in ~/.bashrc than source ~/.bashrc from the folder ~miniconda/bin i call gmx_MMPBSA (base) debanjan@debanjan:~/Amber/amber20/miniconda/bin$ gmx_MMPBSA Traceback (most recent call last): File "/home/debanjan/Amber/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 24, in <module> from GMXMMPBSA import main File "/home/debanjan/Amber/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 44, in <module> from GMXMMPBSA.createinput import create_inputs File "/home/debanjan/Amber/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/createinput.py", line 43, in <module> from parmed.amber.mdin import Mdin ModuleNotFoundError: No module named 'parmed' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "./gmx_MMPBSA", line 5, in <module> from GMXMMPBSA.app import gmxmmpbsa File "/home/debanjan/Amber/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 30, in <module> raise ImportError('Could not import Amber Python modules. Please make sure ' ImportError: Could not import Amber Python modules. Please make sure you have sourced /home/debanjan/Amber/amber20/amber.sh (if you are using sh/ksh/bash/zsh) or /home/debanjan/Amber/amber20/amber.csh (if you are using csh/tcsh) it returns error

…

On Tue, Nov 10, 2020 at 2:31 AM Mario Sergio Valdés Tresanco < ***@***.***> wrote: Ok the problem is that amber.python does not detect the parmed module. This is probably because the python modules are not in the default path or the amber source has not been done correctly. Try adding this line to your .bashrc file /home/debanjan/Amber/amber20/amber.sh — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOJ7Q4VGEJ43XDEMKIQE5I3SPBKCRANCNFSM4TPSIC3A> .

[Valdes-Tresanco-MS]

Please, check the PYTHONPATH variable
echo $PYTHONPATH

[debanjansen48]

(base) debanjan@debanjan:~$ echo $PYTHONPATH /home/debanjan/MGLTools-1.5.7/bin/python

…

On Tue, Nov 10, 2020 at 3:03 AM Mario Sergio Valdés Tresanco < ***@***.***> wrote: Please, check the PYTHONPATH variable echo $PYTHONPATH — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOJ7Q4R3I6B4NUEDFKS5BLLSPBNY7ANCNFSM4TPSIC3A> .

[debanjansen48]

i removed this path "/home/debanjan/MGLTools-1.5.7/bin/python" (base) debanjan@debanjan:~/Desktop$ echo $PYTHONPATH /home/debanjan/Amber/amber20/lib/python3.8/site-packages:/home/debanjan/amber18/lib/python2.7/site-packages:/home/debanjan/pDynamo-1.9.0/pBabel-1.9.0:/home/debanjan/pDynamo-1.9.0/pCore-1.9.0:/home/debanjan/pDynamo-1.9.0/pGraph-0.1:/home/debanjan/pDynamo-1.9.0/pMolecule-1.9.0:/home/debanjan/pDynamo-1.9.0/pMoleculeScripts-1.9.0 On Tue, Nov 10, 2020 at 3:07 AM Debanjan Sen <debanjansen48@gmail.com> wrote:

…

(base) ***@***.***:~$ echo $PYTHONPATH /home/debanjan/MGLTools-1.5.7/bin/python On Tue, Nov 10, 2020 at 3:03 AM Mario Sergio Valdés Tresanco < ***@***.***> wrote: > Please, check the PYTHONPATH variable > echo $PYTHONPATH > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#2 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AOJ7Q4R3I6B4NUEDFKS5BLLSPBNY7ANCNFSM4TPSIC3A> > . >

[debanjansen48]

Yahhhhhhhhhh!!!!!!!!!!!!!!!!!!!! ITS WORKING NOW............... (base) debanjan@debanjan:~/Amber/amber20/miniconda/bin$ gmx_MMPBSA InputError: No input file was provided! Enter `gmx_MMPBSA --help` for help shall i move gmx_MMPBSA to /usr/local/bin or how to call gmx_MMPBSA from any location sir? On Tue, Nov 10, 2020 at 3:09 AM Debanjan Sen <debanjansen48@gmail.com> wrote:

…

i removed this path "/home/debanjan/MGLTools-1.5.7/bin/python" (base) ***@***.***:~/Desktop$ echo $PYTHONPATH /home/debanjan/Amber/amber20/lib/python3.8/site-packages:/home/debanjan/amber18/lib/python2.7/site-packages:/home/debanjan/pDynamo-1.9.0/pBabel-1.9.0:/home/debanjan/pDynamo-1.9.0/pCore-1.9.0:/home/debanjan/pDynamo-1.9.0/pGraph-0.1:/home/debanjan/pDynamo-1.9.0/pMolecule-1.9.0:/home/debanjan/pDynamo-1.9.0/pMoleculeScripts-1.9.0 On Tue, Nov 10, 2020 at 3:07 AM Debanjan Sen ***@***.***> wrote: > (base) ***@***.***:~$ echo $PYTHONPATH > /home/debanjan/MGLTools-1.5.7/bin/python > > On Tue, Nov 10, 2020 at 3:03 AM Mario Sergio Valdés Tresanco < > ***@***.***> wrote: > >> Please, check the PYTHONPATH variable >> echo $PYTHONPATH >> >> — >> You are receiving this because you authored the thread. >> Reply to this email directly, view it on GitHub >> <#2 (comment)>, >> or unsubscribe >> <https://github.com/notifications/unsubscribe-auth/AOJ7Q4R3I6B4NUEDFKS5BLLSPBNY7ANCNFSM4TPSIC3A> >> . >> >

[Valdes-Tresanco-MS]

Excellent. I will try to optimize the process for future reference.
I will add a section in the documentation for new users. Thanks for reporting the problem.
Enjoy it

[Valdes-Tresanco-MS]

Oh sorry I forgot the warning !!!
This warning is because pip installs the executables (gmx_MMPBSA and gmx_MMPBSA_gui) in */amber20/miniconda/bin.
You have two options to solve this:

Add this folder (*/amber20/miniconda/bin) to PATH:
export PATH="/home/mario/programs/amber20/miniconda/bin:$PATH"
or
initializing the environment of conda amber:
amber.conda init bash

You can deactivate like this:
conda deactivate

[debanjansen48]

thanks... I found in the literature that u mentioned in git... there are options for Amber forcefields .... I did 3 MD simulations (protein ligand and it's the repetation) using CHARMM36 force field and 2 simulations (repetation) using OPLS AA forcefield.. 1. shall I calculate thermo data for Charmm36 trajectories? 2. shall I calculate the same for OPLS trajectories? 3. It was mentioned ligand simulation data required.. Shall I need to run the simulation for solo ligand (protein free ligand)? please Assist... I must acknowledge, it's a great pakage for Gromacs users...

…

On Tue, 10 Nov 2020, 3:30 am Mario Sergio Valdés Tresanco, < ***@***.***> wrote: Oh sorry I forgot the warning !!! This warning is because pip installs the executables (gmx_MMPBSA and gmx_MMPBSA_gui) in */amber20/miniconda/bin. You have two options to solve this: Add this folder (*/amber20/miniconda/bin) to PATH: export PATH="/home/mario/programs/amber20/miniconda/bin:$PATH" or initializing the environment of conda amber: amber.conda init bash You can deactivate like this: conda deactivate — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOJ7Q4SOSTVIDO3VH27QFFTSPBRBHANCNFSM4TPSIC3A> .

[Valdes-Tresanco-MS]

Sorry, only amber force fields are supported at the moment. We will do our best to implement the Charmm force field.
I'm not sure if OPLS is supported by Amber, I'll check

3. Actually it refers to the mol2 file that is obtained from the ligand parameterization (small molecule) with antechamber. This file contains the data (charges, type and bond order, atom type, etc.) to generate the ligand topology.

If you want to do the Single trajectory approach then you only require the complex dynamics and if the ligand is a small molecule the mol2 file. If, on the other hand, you want to do it using Multiple trajectory, then you require the complex, receptor and ligand data.