Error while running gmx

Dr. Shine D

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Apr 30, 2021, 10:29:49 AM4/30/21

to gmx_MMPBSA

Dear all,

I am quiet new to this tool. I have my Gromacs 2021 MD results (Protein-ligand complex: Protein- Charm36 FF, where ligand FF generated externally) for PB/GB calculation using gmx_MMPPSA method, installed the program through Amber20 tools.

I am getting the error while generating results using the input fie as shown below:

-----------------------------------------------------------------

&general

startframe=49000, endframe=50000, verbose=2,

protein_forcefield="./charmm36-jul2020.ff/forcefield.itp", ligand_forcefield="ligand.top"

/

&pb

# radiopt=0 is recommended which means using radii from the prmtop file

# for both the PB calculation and for the NP calculation

istrng=0.15, fillratio=4.0, radiopt=0

/

------------------------------

Command

----------------------------------

gmx_MMPBSA -i mmpbsa.in -cs md_run_final.tpr -ct md_run_nopbc.xtc -rs receptor.gro -ls LIG.gro -cp topol.top -lp ligand.top

----------------------------

Error

------------------

[INFO ] Starting

[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead.

----

--------

[INFO ] Using GROMACS version > 5.x.x!

[INFO ] gmx found! Using /usr/local/gromacs/bin/gmx

[INFO ] Checking external programs...Done.

[INFO ] Building AMBER Topologies from GROMACS files...

[INFO ] Checking if supported force fields exists in Amber data...

[ERROR ] MMPBSA_Error You must define the structure, topology and index files, as well as the groups!.

Check the gmx_MMPBSA.log file to report the problem.

File "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/bin/gmx_MMPBSA", line 8, in <module>

sys.exit(gmxmmpbsa())

File "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 97, in gmxmmpbsa

app.make_prmtops()

File "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 576, in make_prmtops

maketop = CheckMakeTop(self.FILES, self.INPUT, self.external_progs)

File "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 99, in __init__

self.checkFiles()

File "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 104, in checkFiles

GMXMMPBSA_ERROR('You must define the structure, topology and index files, as well as the groups!')

File "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__

raise exc(msg + '. Check the gmx_MMPBSA.log file to report the problem.')

MMPBSA_Error: You must define the structure, topology and index files, as well as the groups!. Check the gmx_MMPBSA.log file to report the problem.

Exiting. All files have been retained.

-----------------------

Kindly give your suggestion

Thank you

Mario Sergio Valdes

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Apr 30, 2021, 10:38:29 AM4/30/21

to gmx_MMPBSA

Hi and welcome!

In your case, there are several inconsistencies.

Its system is Protein-ligand using CHARMM force field. The generation of the topology is done through the conversion of Gromacs to Amber, so the definition of protein_forcefield or ligand_forcefield is not required.

If you use the Single Trajectory approach (only define the trajectory of the complex), you don't need to define the topology of the ligand.

We have several examples in the documentation, as well as the definition of all variables, please check it

Charmm example: https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/Protein_ligand_CHARMMff/

Variable definition: https://valdes-tresanco-ms.github.io/gmx_MMPBSA/input_file/

HTH!

Mario S.

Dr. Shine D

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May 1, 2021, 6:53:47 AM5/1/21

to gmx_MMPBSA

Thank you for the suggestion. This time I haven't mentioned any topology file, but error come as:

/amber20/bin/tleap failed when querying _GMXMMPBSA_leap.in. Check the gmx_MMPBSA.log file to report the problem.

---------------

mmpbsa.in

&general

startframe=1000, endframe=2000, verbose=2,

/

&pb

# radiopt=0 is recommended which means using radii from the prmtop file

# for both the PB calculation and for the NP calculation

istrng=0.15, fillratio=4.0, radiopt=0

/

-------

command

gmx_MMPBSA -O -i mmpbsa.in -cs md_run_final.tpr -ci index.ndx -cg 1 13 -ct md_run_nopbc.xtc

-------------------

So any guidelines to track it.

regards

Mario Sergio Valdes

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May 1, 2021, 11:36:58 AM5/1/21

to gmx_MMPBSA

This is expected since the ligand was independently parameterized. If the ligand is a small molecule and not topology was defined then you must define the mol2 file (the antechamber output) with the -lm option. See how this process works here (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/howworks/). Note that this process will not work for the charmm force field or instead you can estimate the energy with a different force field than the one used in the simulation which can give you a totally ambiguous result.

If your system is about protein-ligand with the charmm force field, please refer to the example that we have provided in the documentation (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/Protein_ligand_CHARMMff/)

HTH!

Mario S.

Dr. Shine D

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May 5, 2021, 12:58:01 PM5/5/21

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Hello,

While performing gmx_MMPBSA_test Prot_lig_charmm, not able to finish the calculation..getting error like this, how to install the same to visualize the result

[INFO ] Example STATE

--------------------------------------------------------------------------------

[INFO ] Protein-Ligand (CHARMM force field) RUNNING

[INFO ] Protein-Ligand (CHARMM force field) [ 1/ 1] DONE

--------------------------------------------------------------------------------

[INFO ] Opening gmx_MMPBSA_ana...

qt.qpa.xcb: could not connect to display

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.

This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

Mario Sergio Valdes

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May 5, 2021, 1:14:48 PM5/5/21

to gmx_MMPBSA

What OS are you using?

The calculation completed successfully as shown in the log. gmx_MMPBSA_ana works as a standalone application, so its failure to start does not affect the calculations at all. A similar error was reported earlier and we resolved it by reinstalling the libxcb library:

sudo apt install --reinstall libxcb-xinerama0

HTH!

Mario S.

Dr. Shine D

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May 6, 2021, 12:58:01 AM5/6/21

to gmx_MMPBSA

OS is Ubuntu 20.04 LTS

After using sudo apt install --reinstall libxcb-xinerama0,

I tried with gmx_MMPBSA_ana ... but core dumped..

(gmx_MMPBSA_ana -h to check this is working)

------

qt.qpa.xcb: could not connect to display

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.

This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

Aborted (core dumped)

---------

And xcb is present: libxcb-xinerama0 is already the newest version (1.14-2).

Tried to resolve using various suggestions but nothing works for me to in this case.

Regards

Mario Sergio Valdes

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May 6, 2021, 1:23:46 AM5/6/21

to gmx_MMPBSA

Please try installing/reinstalling zlib and then PyQt5

sudo apt install zlib or sudo apt install --reinstall zlib

amber.python -m pip uninstall PyQt5 and then amber.python -m pip install PyQt5

If it still doesn't work, please run this and send me the output

export QT_DEBUG_PLUGINS = 1

gmx_MMPBSA_ana -h

Best!

Mario S.

Dr. Shine D

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May 11, 2021, 5:36:11 AM5/11/21

to gmx_MMPBSA

Hello,

Here is the output as I have tried this option, but same error while running gmx_MMPBSA_ana

root@DESKTOP-G6S8A0U:/mnt/d/Dr.Jyoti-proj/amber20/Retinovir# export QT_DEBUG_PLUGINS=1

root@DESKTOP-G6S8A0U:/mnt/d/Dr.Jyoti-proj/amber20/Retinovir#

------------------

root@DESKTOP-G6S8A0U:/mnt/d/Dr.Jyoti-proj/amber20/Retinovir# gmx_MMPBSA_ana -h

QFactoryLoader::QFactoryLoader() checking directory path "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms" ...

QFactoryLoader::QFactoryLoader() looking at "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqeglfs.so"

Found metadata in lib /mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqeglfs.so, metadata=

{

"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",

"MetaData": {

"Keys": [

"eglfs"

]

},

"archreq": 0,

"className": "QEglFSIntegrationPlugin",

"debug": false,

"version": 331520

}

Got keys from plugin meta data ("eglfs")

QFactoryLoader::QFactoryLoader() looking at "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqlinuxfb.so"

Found metadata in lib /mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqlinuxfb.so, metadata=

{

"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",

"MetaData": {

"Keys": [

"linuxfb"

]

},

"archreq": 0,

"className": "QLinuxFbIntegrationPlugin",

"debug": false,

"version": 331520

}

Got keys from plugin meta data ("linuxfb")

QFactoryLoader::QFactoryLoader() looking at "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqminimal.so"

Found metadata in lib /mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqminimal.so, metadata=

{

"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",

"MetaData": {

"Keys": [

"minimal"

]

},

"archreq": 0,

"className": "QMinimalIntegrationPlugin",

"debug": false,

"version": 331520

}

Got keys from plugin meta data ("minimal")

QFactoryLoader::QFactoryLoader() looking at "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqminimalegl.so"

Found metadata in lib /mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqminimalegl.so, metadata=

{

"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",

"MetaData": {

"Keys": [

"minimalegl"

]

},

"archreq": 0,

"className": "QMinimalEglIntegrationPlugin",

"debug": false,

"version": 331520

}

Got keys from plugin meta data ("minimalegl")

QFactoryLoader::QFactoryLoader() looking at "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqoffscreen.so"

Found metadata in lib /mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqoffscreen.so, metadata=

{

"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",

"MetaData": {

"Keys": [

"offscreen"

]

},

"archreq": 0,

"className": "QOffscreenIntegrationPlugin",

"debug": false,

"version": 331520

}

Got keys from plugin meta data ("offscreen")

QFactoryLoader::QFactoryLoader() looking at "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqvnc.so"

Found metadata in lib /mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqvnc.so, metadata=

{

"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",

"MetaData": {

"Keys": [

"vnc"

]

},

"archreq": 0,

"className": "QVncIntegrationPlugin",

"debug": false,

"version": 331520

}

Got keys from plugin meta data ("vnc")

QFactoryLoader::QFactoryLoader() looking at "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-egl.so"

Found metadata in lib /mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-egl.so, metadata=

{

"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",

"MetaData": {

"Keys": [

"wayland-egl"

]

},

"archreq": 0,

"className": "QWaylandEglPlatformIntegrationPlugin",

"debug": false,

"version": 331520

}

Got keys from plugin meta data ("wayland-egl")

QFactoryLoader::QFactoryLoader() looking at "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-generic.so"

Found metadata in lib /mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-generic.so, metadata=

{

"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",

"MetaData": {

"Keys": [

"wayland"

]

},

"archreq": 0,

"className": "QWaylandIntegrationPlugin",

"debug": false,

"version": 331520

}

Got keys from plugin meta data ("wayland")

QFactoryLoader::QFactoryLoader() looking at "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-egl.so"

Found metadata in lib /mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-egl.so, metadata=

{

"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",

"MetaData": {

"Keys": [

"wayland-xcomposite-egl"

]

},

"archreq": 0,

"className": "QWaylandXCompositeEglPlatformIntegrationPlugin",

"debug": false,

"version": 331520

}

Got keys from plugin meta data ("wayland-xcomposite-egl")

QFactoryLoader::QFactoryLoader() looking at "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-glx.so"

Found metadata in lib /mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-glx.so, metadata=

{

"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",

"MetaData": {

"Keys": [

"wayland-xcomposite-glx"

]

},

"archreq": 0,

"className": "QWaylandXCompositeGlxPlatformIntegrationPlugin",

"debug": false,

"version": 331520

}

Got keys from plugin meta data ("wayland-xcomposite-glx")

QFactoryLoader::QFactoryLoader() looking at "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwebgl.so"

Found metadata in lib /mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwebgl.so, metadata=

{

"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",

"MetaData": {

"Keys": [

"webgl"

]

},

"archreq": 0,

"className": "QWebGLIntegrationPlugin",

"debug": false,

"version": 331520

}

Got keys from plugin meta data ("webgl")

QFactoryLoader::QFactoryLoader() looking at "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so"

Found metadata in lib /mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so, metadata=

{

"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",

"MetaData": {

"Keys": [

"xcb"

]

},

"archreq": 0,

"className": "QXcbIntegrationPlugin",

"debug": false,

"version": 331520

}

Got keys from plugin meta data ("xcb")

QFactoryLoader::QFactoryLoader() checking directory path "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/bin/platforms" ...

loaded library "/mnt/d/Dr.Jyoti-proj/amber20/miniconda/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so"

qt.qpa.xcb: could not connect to display

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.

This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

Aborted (core dumped)

Mario Sergio Valdes

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May 11, 2021, 11:52:30 PM5/11/21

to gmx_MMPBSA

Dear Dr Shine.

Sorry for the delay. Since the problem is not resolved, then I have had to spend a lot of time installing and testing Ubuntu 20.04.

After installing Ubuntu 20.04 (virtual machine) I managed to reproduce the error. However, the error was completely fixed with the command I sent you earlier. (sudo apt install --reinstall libxcb-xinerama0)

Are you using Ubuntu 20.04 natively or on the Windows Subsystem Linux?

Unfortunately, I cannot fully reproduce these types of errors since I have no way to explore all their variants.

I recommend you try some of the solutions they propose in this thread (https://askubuntu.com/questions/308128/failed-to-load-platform-plugin-xcb-while-launching-qt5-app-on-linux-without )

Best!

Mario S.

Mario Sergio Valdes

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May 12, 2021, 1:34:59 AM5/12/21

to gmx_MMPBSA

Closing of the discussion.

The error related to the qt5 graphics library is due to trying to run gmx_MMPBSA_ana on the Windows Subsystem for Linux (WSL). The WSL has no graphics drivers so it is impossible to run native Linux graphics applications. Therefore, there is currently no way to run gmx_MMPBSA_ana in such an environment.

If your OS is any native Linux distribution (not WSL, HPC, or older Centos and Debian versions) this error should be fixed with the commands described above.

Alternatively, you can run gmx_MMPBSA in WSL and create a virtual machine to run gmx_MMPBSA_ana

Error while running gmx_MMPBSA

Dr. Shine D

Mario Sergio Valdes

Dr. Shine D

Mario Sergio Valdes

Dr. Shine D

Mario Sergio Valdes

Dr. Shine D

Mario Sergio Valdes

Dr. Shine D

Mario Sergio Valdes

Mario Sergio Valdes