gmx_MMPBSA installation error with centOS 8

[fred]

Dear all, since gmx_MMPBSA_ana is not available for ubuntu, i therefore created a virtual box with centOS 7 system to access it.  However, installation of gromacs is unsuccessful as it cant recognize CXX17 language. in view of this, i have switched the virtual box OS to centOS 8  in centOS 8, installations of gromacs, ambertools21 and pytq5 are perfectly fine. however, when i try to install the  openmpi-bin, libopenmpi-dev,  and openssh-client , no package was found for the respective installation. Thus, i have put down the command "yum install openmpi" and "yum install openssh" to install those dependencies. the version of openmpi and openssh are 4.0.5 and 8.0p1 respectively.  May i know is that fine for gmx_MMPBSA installation?

After installing both openmpi and openssh, i proceed to the installation of gmx_MMPBSA using  command "python3 -m pip install gmx_MMPBSA". Then, error occur as following:

collecting scipy>=1.6.1 (from gmx_MMPBSA)

  Could not find a version that satisfies the requirement scipy>=1.6.1 (from gmx_MMPBSA) (from versions: 0.8.0, 0.9.0, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.12.1, 0.13.0, 0.13.1, 0.13.2, 0.13.3, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.16.0, 0.16.1, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 1.0.0b1, 1.0.0rc1, 1.0.0rc2, 1.0.0, 1.0.1, 1.1.0rc1, 1.1.0, 1.2.0rc1, 1.2.0rc2, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.3.0rc1, 1.3.0rc2, 1.3.0, 1.3.1, 1.3.2, 1.3.3, 1.4.0rc1, 1.4.0rc2, 1.4.0, 1.4.1, 1.5.0rc1, 1.5.0rc2, 1.5.0, 1.5.1, 1.5.2, 1.5.3, 1.5.4)

No matching distribution found for scipy>=1.6.1 (from gmx_MMPBSA)

May i know is there any solution for this? any ways to reduce the scipy? i have tried twice using lower and higher version of python3 but all (3.6. 3.8 and 3.9) has failed to overcome this problem.  Please guide me in solving this issue. Thanks for the helps in advance.

Fred

[Mario Sergio Valdes]

Hi Fred...

What version of ubuntu are you using? gmx_MMPBSA, as well as gmx_MMPBSA_ana and gmx_MMPBSA_test, have been tested on various Ubuntu versions (18.04 and 20.04) and are working correctly. It has also been tested on various versions of Linux Mint (19.3 and 20.2), Kubuntu (20.04), Debian 9, Centos8, and macOS BigSur. Of these, there are compatibility issues on macOS < BigSur and on Centos and Debian as described in the Q&A (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/Q%26A/OS_issues/)

Centos and Debian are aimed at servers so their libraries are very stable but somewhat old, so installing the modern versions of GROMACS and other dependencies of gmx_MMPBSA becomes very complicated. gmx_MMPBSA itself works correctly, gmx_MMPBSA_ana has the problem due to the incompatibility between the graphic libraries and PyQt5

The scipy compatibility error, I assume is OS-related, because in all the times we have tried it, this error has not been caught.

We don't recommend working with gmx_MMPBSA_ana on Centos or Debian unless you know how to handle all dependencies manually. Due to the enormous effort involved in program maintenance, we only ensure command line execution support for these OSs.

Try to install it on Ubuntu and report any errors you get to help you.

Cheers!

Mario S.

[fred]

Hi Mario,

Thanks for your reply. I have switched the system to Ubuntu desktop and everything goes well. However, may i know is it possible to run gmx_MMPBSA in host system and analyze the result using gmx_MMPBSA_ana with virtual system? i have shared the calculated data from host system to Ubuntu virtual system. However, when i perform gmx_MMPBSA_ana, errors occurred as follow:

Traceback (most recent call last):

  File "/usr/lib/python3.8/multiprocessing/pool.py", line 125, in worker

    result = (True, func(*args, **kwds))

  File "/home/bionfo/.local/lib/python3.8/site-packages/GMXMMPBSA/analyzer/utils.py", line 33, in calculatestar

    return run_process(*args)

  File "/home/bionfo/.local/lib/python3.8/site-packages/GMXMMPBSA/analyzer/utils.py", line 37, in run_process

    results = func(path)

  File "/home/bionfo/.local/lib/python3.8/site-packages/GMXMMPBSA/API.py", line 384, in load_gmxmmpbsa_info

    return_data = mmpbsa_data(app)

  File "/home/bionfo/.local/lib/python3.8/site-packages/GMXMMPBSA/API.py", line 89, in __init__

    for key in app.calc_types['mutant']:

KeyError: 'mutant'

"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):

  File "/home/bionfo/.local/lib/python3.8/site-packages/GMXMMPBSA/analyzer/utils.py", line 61, in run

    for result in imap_unordered_it:

  File "/usr/lib/python3.8/multiprocessing/pool.py", line 868, in next

    raise value

KeyError: 'mutant'

Aborted (core dumped)

any ideas how to solve this？ Thanks in advance!

Fred

[Mario Sergio Valdes]

Hi Fred.

gmx_MMPBSA works on server and HPC systems without problems, however, gmx_MMPBSA_ana does not. This is because gmx_MMPBSA_ana uses the latest version of PyQt5 and these OS have the graphics drivers disabled. gmx_MMPBSA_ana works correctly, as long as the graphics drivers allow it, so it must work correctly in a VM. Remember that a VM works with the virtualization of the OS, so its drivers depend on the OS it is running on

I can't solve this error without more information. What version of gmx_MMPBSA are you using? Use the version (1.4.3) available in pip since the Github version is in development and can be unstable

If possible send me the files (* .ndx, * .tpr, 10 frames * .xtc, the groups, and the mmpbsa.in file) to check if this is a bug or an input problem

Cheers

Mario S

[fred]

Dear Mario,

I am using v1.4.3 for gmx_MMPBSA with following command

"gmx_MMPBSA -O -i mmpbsa_1500to2000.in -cs str_noLP.pdb -ci index_mod_gromacs.ndx -cg 1 24 -ct com_traj.xtc -cp topol.top"

The calculation was fine and the analyzer was called out. However, when i clicked on the accept tab, the analyzer collapsed with mutant error occurred. in order to rule out the possibility of error caused by file transferring, i have redo the calculation with the virtual system. unfortunately, as in the host system, calculation can be done but analyzer wont be able to be used, 

please obtain those files from my google drive at (https://drive.google.com/drive/folders/1mNMyzQMi3BTKciQpxiISEkcErK8QEIRl?usp=sharing). 

*in the shared folder,  com_traj.xtc, index_mod_gromacs.ndx and str_noLP.pdb are for LP removed trajectory while md_0_20_fit.xtc and md_0_20.tpr are for the initial MD (without removing LP).

Wondering is it related to LP. Thank you so much for your helps!

Fred

[Mario Sergio Valdes]

Please, send me the charmm topology folder

[fred]

Dear Mario,

i have uploaded the charmm folder into my drive. Thank you so much!

fred

[Mario Sergio Valdes]

But not include the py6f.prm file. Please send me this file...

Sorry, i forgot it

[fred]

Hi Mario, I have uploaded py6f.prm to the drive. Thanks again for the helps. 

[fred]

Hi mario,

is there any solutions for my gmx_mmpbsa_ana problem? 

Meanwhile, i have another question. i am interested to calculate interaction energy of each frame. may i know how to get his done? is there anyway to do it with  only 1 calculation or i have to calculate frame by frame?

Regards 

fred 

[Mario Sergio Valdes]

Sorry, but I was never able to reproduce the problem. Please update the shared folder information with the files (10frames xtc, ndx, tpr, groups, and the toppar folder with all itp and prm)

As for the energy per frame, it is not necessary to do it again. gmx_MMPBSA_ana allows you to view the energy per frame (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/analyzer/#line-plot). If you are familiar with python, you can access this information using the API. In extreme cases, you can rerun the calculations using the -eo option to save the data in csv format.

[fred]

Hi mario, i have re-run the calculation with -eo which gave me the data in CSV format. Thanks for the helps. However, since my  gmx_MMPBSA_ana is not working, may i know is there any way/command that allows me to view the contribution of each residue in CSV format? 

Thanks

Fred

[marioe911116]

you can open the *.csv with excel, libre office calculator... the *.csv contains all the information for the receptor, ligand, and the complex as well as the difference. IF you have any doubt, feel free to send the file and I can label the important parts...

cheers!