Unbale to install GMX_MMPBSA for Ambertools 21.3

[S.R. Vignesh]

Sir, 

I want to perform MM-PBSA analysis for my protein-ligand. I installed Ambertools 21.3 via anaconda, inorder to work with gmx_MMPBSA. In ambertools environment, when i try to install "amber.python -m pip install PyQt5", it results in "amber.python command found". I tried few times by reinstalling ambertools, but i am unable to rectify this, kindly help me. 

PS: Kindly upload, installation video for gmx_MMPBSA, it will be useful for us.

Thanks in advance

[Mario Sergio Valdes]

Hi and welcome!

amber.python corresponds to Amber's conda environment python when compiled directly. However, in your case, since you installed ambertool through a predefined conda environment, gmx_MMPBSA must be installed with the same interpreter. That is, install the required modules as well as gmx_MMPBSA with the python interpreter from your conda environment

conda activate AmberTools21

python -m pip install PyQt5 gmx_MMPBSA

Note that if you have an active conda environment, it must be active in order to access the gmx_MMPBSA applications

HTH!

Mario S.

[S.R. Vignesh]

Hai Sir, thank you very much for your reply, i tried the above given commands, PyQt5 is installed but unable to install gmx_MMPBSA, Sir. I have attached the error message below, kindly help me, Sir.

Thank you Sir and have a nice day

[Mario Sergio Valdes]

Did you run the OpenMPI installation?

To rule out that the error is due to an incompatibility with the conda libraries (which should not happen and we have never seen) execute the command:

sudo apt install openmpi-bin libopenmpi-dev openssh-client

or if it is already installed

sudo apt install --reinstall openmpi-bin libopenmpi-dev openssh-client

If you install the OpenMPI libraries correctly, then run the gmx_MMPBSA installation

HTH!

Mario S.

[S.R. Vignesh]

Thank you sir for replying, 

i reinstalled openmpi and its libraries, again i am getting the same errors, sir.. kindly check the error message given below. Thank you Sir

[Mario Sergio Valdes]

Now that I realize it, it seems that your version of the OpenMPI library (2.1.1) is not compatible with version 3.x of mpi4py.

What version of Ubuntu (or derivative) are you using?

You can try to satisfy the mpi4py installation requirement, installing it from conda (conda install -c anaconda mpi4py)

HTH

Mario S.

[S.R. Vignesh]

Hello Sir, thanks for your response.

I am using Ubuntu 18.04.

I tried "conda install -c anaconda mpi4py"

but still the error is same, kindly view the error file attatched.

Thank you, Sir

[Mario Sergio Valdes]

Please try to install the mpi in your AmberTools21 conda environment as follow:

conda install -c anaconda -n AmberTools21 mpi4py or 

conda install -n AmberTools21 mpi4py

In any case, I am installing a virtual machine to try to reproduce the problem, since it is the first time something like this has happened. Please be patient, we will try to help you solve the problem

HTH!

Mario S.

[S.R. Vignesh]

Thank you Sir, for your wonderful service..

I tried "conda install -n AmberTools21 mpi4py "

The message, i got is:

//

(AmberTools21) srv@srv-ps:~$ conda install -c anaconda -n AmberTools21 mpi4py

Collecting package metadata (repodata.json): done

Solving environment: failed with initial frozen solve. Retrying with flexible solve.

Solving environment: - 

Found conflicts! Looking for incompatible packages.

This can take several minutes.  Press CTRL-C to abort.

failed                                                                          

UnsatisfiableError: The following specifications were found

to be incompatible with the existing python installation in your environment:

Specifications:

  - mpi4py -> python[version='>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0']

Your python: python=3.9

If python is on the left-most side of the chain, that's the version you've asked for.

When python appears to the right, that indicates that the thing on the left is somehow

not available for the python version you are constrained to. Note that conda will not

change your python version to a different minor version unless you explicitly specify

that.

//

So i tried to downgrade the python version (to python 3.7 [is it wrong?]) in Ambertools 21 alone (Conda Version of python is 3.7, while Ambertools version is 3.9)

I got a huge error, kindly check the file below.

I wholeheartedly appreciate your efforts, Sir.. 

Thank you, Sir and have a nice day

[Mario Sergio Valdes]

Downgrade the python version in conda should not be done under any circumstances, since it conflicts with all the installed packages, as in your case. We have users with python3.9 in conda environments who have correctly installed gmx_MMPBSA. Maybe they have done it on higher versions of ubuntu. I will try to find the problem.

If possible, it would be very helpful to know if this problem is also present with the compiled version of AmberTools. Please, if you carry out this installation, follow the instructions mentioned in https://ambermd.org/InstUbuntu.php, installing the dependencies before running cmake

Mario S.

[S.R. Vignesh]

Sir,  i am using my system for my simulation studies and my unpublished data are it. I feel conda is safe option for installing ambertools (conda install -c conda-forge ambertools [ but this command installed ambertools 19.10 in my system]) let me try to arrange a computer for installing Ambertools compiled version, if i can succeed, let me inform you, Sir..

Thank you, sir

[S.R. Vignesh]

Sir, now i freshly installed Ambertools, as per the procedure give in http://ambermd.org/GetAmber.php#ambertools for conda environment, still i face the error for downgrading python, here i included the terminal's result. 

Thank you sir.

[Mario Sergio Valdes]

I have already identified the problem.

When creating the virtual environment for Ambertools21, the python base of anaconda/miniconda is updated from version 3.8.5 to 3.9.5. MPI4PY is not compatible with versions higher than 3.9.0 so it conflicts.

The solution is to install mpi4py directly from Github

conda activate AmberTools21

python -m pip install git+https://github.com/mpi4py/mpi4py

python -m pip install PyQt5 gmx_MMPBSA

It should continue smoothly

HTH!

Mario S.

[Mario Sergio Valdes]

After reporting the problem and doing some tests to provide the corresponding information to the mpi4py developer, I have identified the possible causes.

If you install the compilers package, mpi4py fails to install using pip, since it uses the system compiler and the headers (definition files) of the conda environment. However, you can install mpi4py from conda to satisfy the requirement:

conda activate AmberTools21

conda install -c conda-forge ambertools = 21 compilers

conda install -c conda-forge mpi4py

then install gmx_MMPBSA (python -m pip install gmx_MMPBSA)

If not, you can skip the compilers package which is not required, or simply change the installation order to:

conda activate AmberTools21

conda install -c conda-forge ambertools = 21

python -m pip install mpi4py

conda install -c conda-forge compilers

python -m pip install gmx_MMPBSA

HTH!

Mario S.

[S.R. Vignesh]

Thank you so much sir, your work is awesome.

gmx_MMPBSA installed successfully..

Thank you Sir, again.

[Mario Sergio Valdes]

Excellent. I will add these indications to the documentation for users who may have this error.

We are about to release version 1.5.0 that comes with several interesting features ...

I hope you enjoy gmx_MMBSA and find it useful.

Best wishes!

Mario S.

[S.R. Vignesh]

Great Sir, best wishes for you and your team..

Thank you Sir.