How to Set up MMPBSA in Gromacs 2024.1

User discussions
,
1

GROMACS version: 2024.1
GROMACS modification: No
Guide me please to install and run MMPBSA in Gromacs 2024.1, I have found which is a version of 2021, will that work on Gromacs 24? Guide me please…

2

g_MMPBSA only works until gromacs 2020. If u want to do MMPBSA assay using modern version of gromacs you can use gmxMMPBSA - Home - gmx_MMPBSA Documentation. The installation guide is in the website.

3

I’m facing issue during installation of gmx_MMPBSA, the error states - ```
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pandas
Failed to build pandas
ERROR: Could not build wheels for pandas, which is required to install pyproject.toml-based projects


please help me..
4

You need to install pandas. Activate the environment by typing conda activate gmxMMPBSA (if you have named the environment same as in the tutorial) and then install pandas by typing in pip install pandas.

5

I get this - after the comand “pip install pandas”

Requirement already satisfied: pandas in /home/khaten/anaconda3/envs/gmxMMPBSA/lib/python3.10/site-packages (3.0.0.dev0+1173.gdcb5494e5)
Requirement already satisfied: numpy>=1.23.5 in /home/khaten/anaconda3/envs/gmxMMPBSA/lib/python3.10/site-packages (from pandas) (2.0.0)
Requirement already satisfied: python-dateutil>=2.8.2 in /home/khaten/anaconda3/envs/gmxMMPBSA/lib/python3.10/site-packages (from pandas) (2.9.0)
Requirement already satisfied: pytz>=2020.1 in /home/khaten/anaconda3/envs/gmxMMPBSA/lib/python3.10/site-packages (from pandas) (2024.1)
Requirement already satisfied: tzdata>=2022.7 in /home/khaten/anaconda3/envs/gmxMMPBSA/lib/python3.10/site-packages (from pandas) (2024.1)
Requirement already satisfied: six>=1.5 in /home/khaten/anaconda3/envs/gmxMMPBSA/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas) (1.16.0)

After that I use the command - “python -m pip install gmx_MMPBSA” and I get the same error as earlier…

error: command ‘/usr/bin/gcc’ failed with exit code 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pandas
Failed to build pandas
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (pandas)

Need your help…Thank you.

6

I did some search and i think the issue might be that typing the command pip install pandas does not install it in the environment, rather typing python -m pip install pandas will install the package in the preferred environment. (make sure you activate the environment before installing)

source - “pip install” and “python -m pip install” difference. | by poonam Lekhram | Medium.

7

I’m getting this after the command -
(gmxMMPBSA) khaten@Khaten-AI:~/Desktop$ python -m pip install pandas
Requirement already satisfied: pandas in /home/khaten/anaconda3/envs/gmxMMPBSA/lib/python3.10/site-packages (3.0.0.dev0+1173.gdcb5494e5)
Requirement already satisfied: numpy>=1.23.5 in /home/khaten/anaconda3/envs/gmxMMPBSA/lib/python3.10/site-packages (from pandas) (2.0.0)
Requirement already satisfied: python-dateutil>=2.8.2 in /home/khaten/anaconda3/envs/gmxMMPBSA/lib/python3.10/site-packages (from pandas) (2.9.0)
Requirement already satisfied: pytz>=2020.1 in /home/khaten/anaconda3/envs/gmxMMPBSA/lib/python3.10/site-packages (from pandas) (2024.1)
Requirement already satisfied: tzdata>=2022.7 in /home/khaten/anaconda3/envs/gmxMMPBSA/lib/python3.10/site-packages (from pandas) (2024.1)
Requirement already satisfied: six>=1.5 in /home/khaten/anaconda3/envs/gmxMMPBSA/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas) (1.16.0)

after the command - python -m pip install gmx_MMPBSA
Getting this —

error: command ‘/usr/bin/gcc’ failed with exit code 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pandas
Failed to build pandas
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (pandas)

Is there anyway to install gmxMMPBSA. If you don’t mind can I make a google call via google meet, Please guide…

8

Sure we can have a google meet, i will try to help what i can. Even i’m pretty novice when it come to simulation. mail me-sanjeeva2001ps@gmail.com

9

Did either of you solve this issue? I am having the same problems and would greatly appreciate a fix for this

10

Okay, so the website tutorial has some mistakes in it, Firstly we need to use python 3.9 instead of 3.10 while creating the conda environment in order for it to work and also i believe you need to download older version of amber in order for it to work. If u need any help you can mail me

11

Hi all,

I was having some problems too in the installation.
I was following the instruction at https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/installation/ (install with conda).

I solved the problems I had (I got error messages similar to @KHATEN ) by changing the .yml file they provided (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/env.yml) with the following:

name: gmxMMPBSA
channels:
  - conda-forge
  - defaults
dependencies:
  - python=3.9
  - ambertools<=23.3
  - mpi4py<=3.1.5
  - gromacs<=2023.4
  - git
  - pyqt=5.15.4 
  - pandas=1.2.2  # Install via Conda instead of pip
  - seaborn<0.12
  - scipy>=1.6.1
  - matplotlib=3.5.2
  - tqdm
  - pip
  - pip:
      - gmx-mmpbsa  # Only keep what is not available via Conda

As @ShintY pointed out, it seems to work with python 3.9 and not with 3.10…

I hope this will be helpful for someone else!

cheers

Anna

2 Likes