BFEE2 How to Install BFEE2 VMD Plugin?

Is there a step-by-step tutorial for installing the BFEE2 VMD Plugin?

I tried to install BFEE2 using conda on my Windows machine, but I am running into an issue. I get an error that the module Pyside2 cannot be found:

(base) C:\Users\Christos>python3 C:\Users\Christos\anaconda3\Scripts\BFEE2Gui.py
Traceback (most recent call last):
  File "C:\Users\Christos\anaconda3\Scripts\BFEE2Gui.py", line 43, in <module>
    from PySide2.QtWidgets import QApplication
ModuleNotFoundError: No module named 'PySide2'

However, during the installation process, I can see that pyside2 was installed:

The following NEW packages will be INSTALLED:

  appdirs            conda-forge/noarch::appdirs-1.4.4-pyh9f0ad1d_0
  bfee2              conda-forge/noarch::bfee2-2.3.0-pyhd8ed1ab_0
  biopython          conda-forge/win-64::biopython-1.79-py38h294d835_1
  brotli             conda-forge/win-64::brotli-1.0.9-h8ffe710_7
  brotli-bin         conda-forge/win-64::brotli-bin-1.0.9-h8ffe710_7
  cftime             conda-forge/win-64::cftime-1.6.0-py38hbdcd294_1
  curl               pkgs/main/win-64::curl-7.82.0-h2bbff1b_0
  cycler             conda-forge/noarch::cycler-0.11.0-pyhd8ed1ab_0
  fonttools          conda-forge/win-64::fonttools-4.33.3-py38h294d835_0
  griddataformats    conda-forge/noarch::griddataformats-0.7.0-pyhd8ed1ab_0
  gsd                conda-forge/win-64::gsd-2.5.2-py38hbdcd294_0
  hdf4               conda-forge/win-64::hdf4-4.2.15-h0e5069d_3
  hdf5               conda-forge/win-64::hdf5-1.12.1-nompi_h2a0e4a3_100
  joblib             conda-forge/noarch::joblib-1.1.0-pyhd8ed1ab_0
  kiwisolver         conda-forge/win-64::kiwisolver-1.4.2-py38hbd9d945_1
  libbrotlicommon    conda-forge/win-64::libbrotlicommon-1.0.9-h8ffe710_7
  libbrotlidec       conda-forge/win-64::libbrotlidec-1.0.9-h8ffe710_7
  libbrotlienc       conda-forge/win-64::libbrotlienc-1.0.9-h8ffe710_7
  libclang           conda-forge/win-64::libclang-11.1.0-default_h5c34c98_1
  libcurl            pkgs/main/win-64::libcurl-7.82.0-h86230a5_0
  libnetcdf          conda-forge/win-64::libnetcdf-4.8.1-nompi_h1cc8e9d_101
  libssh2            conda-forge/win-64::libssh2-1.10.0-h680486a_2
  libxslt            conda-forge/win-64::libxslt-1.1.33-h65864e5_2
  libzip             conda-forge/win-64::libzip-1.8.0-hfed4ece_1
  m2w64-gcc-libgfor~ conda-forge/win-64::m2w64-gcc-libgfortran-5.3.0-6
  m2w64-gcc-libs     conda-forge/win-64::m2w64-gcc-libs-5.3.0-7
  m2w64-gcc-libs-co~ conda-forge/win-64::m2w64-gcc-libs-core-5.3.0-7
  m2w64-gmp          conda-forge/win-64::m2w64-gmp-6.1.0-2
  m2w64-libwinpthre~ conda-forge/win-64::m2w64-libwinpthread-git-5.0.0.4634.697f757-2
  matplotlib-base    conda-forge/win-64::matplotlib-base-3.5.1-py38h1f000d6_0
  mdanalysis         conda-forge/win-64::mdanalysis-2.1.0-py38h885f38d_1
  mmtf-python        conda-forge/noarch::mmtf-python-1.1.2-py_0
  mrcfile            conda-forge/noarch::mrcfile-1.3.0-pyh44b312d_0
  msgpack-python     conda-forge/win-64::msgpack-python-1.0.3-py38hbd9d945_1
  msys2-conda-epoch  conda-forge/win-64::msys2-conda-epoch-20160418-1
  munkres            conda-forge/noarch::munkres-1.1.4-pyh9f0ad1d_0
  netcdf4            conda-forge/win-64::netcdf4-1.5.8-nompi_py38h0500770_101
  networkx           conda-forge/noarch::networkx-2.8-pyhd8ed1ab_0
  pandas             conda-forge/win-64::pandas-1.4.2-py38hcc40339_1
  parmed             conda-forge/win-64::parmed-3.4.3-py38heb73c8a_2
  patsy              conda-forge/noarch::patsy-0.5.2-pyhd8ed1ab_0
  pyqt-impl          conda-forge/win-64::pyqt-impl-5.12.3-py38h885f38d_8
  pyqt5-sip          conda-forge/win-64::pyqt5-sip-4.19.18-py38h885f38d_8
  pyqtchart          conda-forge/win-64::pyqtchart-5.12-py38h885f38d_8
  pyqtwebengine      conda-forge/win-64::pyqtwebengine-5.12.1-py38h885f38d_8
  pyside2            conda-forge/win-64::pyside2-5.13.2-py38hadd4fab_7
  scikit-learn       conda-forge/win-64::scikit-learn-1.0.2-py38hb60ee80_0
  scipy              conda-forge/win-64::scipy-1.8.0-py38ha1292f7_1
  seaborn            conda-forge/noarch::seaborn-0.11.2-hd8ed1ab_0
  seaborn-base       conda-forge/noarch::seaborn-base-0.11.2-pyhd8ed1ab_0
  statsmodels        conda-forge/win-64::statsmodels-0.13.2-py38h6f4d8f0_0
  threadpoolctl      conda-forge/noarch::threadpoolctl-3.1.0-pyh8a188c0_0
  unicodedata2       conda-forge/win-64::unicodedata2-14.0.0-py38h294d835_1

In any case, I would prefer to be able to use the VMD plugin but I cannot seem to find any information how to install the extension into VMD.

May 01 '22 05:05 christos-efthymiou

@christos-efthymiou You can find a detailed tutorial here (https://www.nature.com/articles/s41596-021-00676-1).

Regarding your problem, I think that you were opening BFEE2Gui.py using a different Python environment than the one with PySide2.

May 01 '22 06:05 fhh2626

Thank you, using python instead of python3 fixed the problem and the interface opened.

In terms of adding the extension to VMD, the only thing I can find is "Optionally, one can link BFEE2 with VMD through File→Settings. If BFEE2 is not linked with VMD, some input files, e.g., the structure file of the extended water box, cannot be generated automatically." I clicked File and Settings and added the full path to VMD on my computer:

However, when I go into VMD I still do not see BFEE2 in the extensions. Where should it be located? Or is it not an extension that can be viewed/opened in VMD and instead needs to be opened each time in the command line?

Thank you for your help.

May 02 '22 03:05 christos-efthymiou

I also wanted to ask about how to use BFEE to calculate the free binding energy of a protein-protein interaction. When I open the GUI, I do not see an option to choose a protein-protein interaction.

However, on the VMD plugins site here https://www.ks.uiuc.edu/Research/vmd/plugins/bfeestimator/, it shows the ability to select a protein-protein interaction:

Why does the GUI look different on the above site compared to what I see on my computer?

May 03 '22 20:05 christos-efthymiou

@christos-efthymiou BFEE2 is not a VMD extension. It only calls VMD to parse CHARMM-formatted files.

May 04 '22 02:05 fhh2626

I also wanted to ask about how to use BFEE to calculate the free binding energy of a protein-protein interaction. When I open the GUI, I do not see an option to choose a protein-protein interaction.

However, on the VMD plugins site here https://www.ks.uiuc.edu/Research/vmd/plugins/bfeestimator/, it shows the ability to select a protein-protein interaction:

Why does the GUI look different on the above site compared to what I see on my computer?

We have two versions of BFEE. BFEE1 is a VMD extension, and BFEE2 is a Python package that can do lots of things which cannot be handled inside VMD (e.g. support of Amber FF). We suggest you use BFEE2 whenever possible.

May 04 '22 02:05 fhh2626

Thank you for the clarification. In my case, as I would like to calculate the binding energy between two protein chains, do I just randomly assign one chain to be the protein and the other to be the ligand (since protein:protein is not an option in the BFEE2 python package)?

Additionally, how do I designate the selection? For example, I have protein chains A and C in my PDB file. How do I select those in the Other Parameters section?

I tried just using A and C, but I get an error that no selection has been made.

I have just checked the PDB file and I believe I have found the ID I need to provide to designate my selection. However, now when I run the program I get the following error:

C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'altLocs' Using default value of ' '
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'icodes' Using default value of ' '
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'chainIDs' Using default value of ''
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'elements' Using default value of ' '
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM'
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1124: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X'
  warnings.warn("Found missing chainIDs."
[WinError 193] %1 is not a valid Win32 application

How can I fix this?

May 12 '22 18:05 christos-efthymiou

Thank you for the clarification. In my case, as I would like to calculate the binding energy between two protein chains, do I just randomly assign one chain to be the protein and the other to be the ligand (since protein:protein is not an option in the BFEE2 python package)?

Additionally, how do I designate the selection? For example, I have protein chains A and C in my PDB file. How do I select those in the Other Parameters section?

I tried just using A and C, but I get an error that no selection has been made.

I have just checked the PDB file and I believe I have found the ID I need to provide to designate my selection. However, now when I run the program I get the following error:
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'altLocs' Using default value of ' '
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'icodes' Using default value of ' '
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'chainIDs' Using default value of ''
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'elements' Using default value of ' '
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM'
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1124: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X'
  warnings.warn("Found missing chainIDs."
[WinError 193] %1 is not a valid Win32 application
How can I fix this?

try this in VMD (after loading psf and pdb)

set chainA [atomselect top "segname A"]
$chainA set chain A
set chainB [atomselect top "segname B"]
$chainB set chain B
set all [atomselect top all]
$all writepsf all.psf
$all writepdb all.pdb

May 13 '22 13:05 fhh2626

When I check my PDB file (and the PSF file), I see that the two chains seem to be designated by the codes AP1 and CP1:

However, even after entering these codes in the BFEE2 plugin I get this error:

C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'altLocs' Using default value of ' '
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'icodes' Using default value of ' '
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'chainIDs' Using default value of ''
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'elements' Using default value of ' '
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1078: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM'
  warnings.warn("Found no information for attr: '{}'"
C:\Users\Christos\anaconda3\lib\site-packages\MDAnalysis\coordinates\PDB.py:1124: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X'
  warnings.warn("Found missing chainIDs."
[WinError 193] %1 is not a valid Win32 application
[WinError 193] %1 is not a valid Win32 application

To try the commands you suggested in the VMD TK Console, I first loaded the PDB file and PSF file that had been created when I set up a previous simulation using QwikMD. Then, I entered the commands you gave:

However, I am not sure how to proceed from here. Does this create new PDB and PSF files with specific changes made that I should then load into BFEE2? I am just a bit confused and appreciate any help.

May 16 '22 04:05 christos-efthymiou

This is probably an Python installation issue. See for example https://stackoverflow.com/questions/65550077/python-winerror-193-1-is-not-a-valid-win32-application

Jun 15 '22 15:06 fhh2626

BFEE2 BFEE2 copied to clipboard

How to Install BFEE2 VMD Plugin?

BFEE2
BFEE2 copied to clipboard