I am trying to install gmx_MMPBSA ubuntu app on windows.
I used these commands respectively.
sudo apt install openmpi-bin libopenmpi-dev openssh-client
sudo apt-get install python
sudo apt-get install python3-pip
sudo apt-get upgrade
sudo apt-get update
curl -O
https://repo.anaconda.com/miniconda/M
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https://www.youtube.com/redirect?event=video_description&redir_token=QUFFLUhqbUdLME02RlhyTTVFTXB0dkI2UE1kbEluZFJRZ3xBQ3Jtc0ttTHlnX1lLLU9iVEJYNEpxWDdTMlFWbFk4TXVPM3ljVU9EcU90eTJadmVSZ0ZjUEdFWXJlcE5XU2JWNjJnOHFCTUV0dGlhcjh5M01vd0I1dXZ2ZlJpdlp0TUhBbTlpaHFwTVkyTFhjbFlFNTNDLVQ2UQ&q=https%3A%2F%2Frepo.anaconda.com%2Fminiconda%2FMiniconda3-latest-Linux-x86_64.sh&v=rLI1MZ4UnVA>
iniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh
conda update conda
conda create -n gmxMMPBSA python=3.9 -y -q
conda activate gmxMMPBSA
conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers -y -q
python -m pip install git+
https://github.com/Valdes-Tresanco-MS...
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https://www.youtube.com/redirect?event=video_description&redir_token=QUFFLUhqa3ZEc3FHZUh4dTM1Z2c1aklSOXhJSE9JQlNsZ3xBQ3Jtc0tucEs4N2dxRmVrZHN3X2MxaGdFWG5nbWVPQTJGdFltMjJTeTlrZmtIaEFaaHdRRWF2UTd1WGxOU1ZzVlg5ZC1MVWpTeW9XbmZsQkhILWE5YkVmVHk0UGw0cDlJbWpKQ0ZaY1BtSkhvVG4taXpKQTI2VQ&q=https%3A%2F%2Fgithub.com%2FValdes-Tresanco-MS%2FParmEd.git%40v3.4&v=rLI1MZ4UnVA>
python -m pip install pyqt5
python -m pip install gmx_MMPBSA
evertyhing goes well but after gmx_MMPBSA_test it gives error
[INFO ] Cloning gmx_MMPBSA repository in
/mnt/g/Amber/amber20/gmx_MMPBSA_test
Cloning into '/mnt/g/Amber/amber20/gmx_MMPBSA_test'...
remote: Enumerating objects: 19519, done.
remote: Counting objects: 100% (201/201), done.
remote: Compressing objects: 100% (75/75), done.
remote: Total 19519 (delta 77), reused 179 (delta 68), pack-reused 19318
Receiving objects: 100% (19519/19519), 325.44 MiB | 1.52 MiB/s, done.
Resolving deltas: 100% (13750/13750), done.
Checking out files: 100% (678/678), done.
[INFO ] Cloning gmx_MMPBSA repository...Done.
[INFO ] Example
STATE
--------------------------------------------------------------------------------
[INFO ] Protein-Ligand (Single trajectory approximation)
RUNNING
[ERROR ] Protein-Ligand (Single trajectory approximation) [ 1/ 9]
ERROR
Please, check the test log
(/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Protein_ligand/ST/3.log)
[INFO ] Protein-Protein
RUNNING
[ERROR ] Protein-Protein [ 2/ 9]
ERROR
Please, check the test log
(/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Protein_protein/4.log)
[INFO ] Protein-DNA
RUNNING
[ERROR ] Protein-DNA [ 3/ 9]
ERROR
Please, check the test log
(/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Protein_DNA/5.log)
[INFO ] Protein-Glycan
RUNNING
[ERROR ] Protein-Glycan [ 4/ 9]
ERROR
Please, check the test log
(/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Protein_glycan/7.log)
[INFO ] Comp_receptor
RUNNING
[ERROR ] Comp_receptor [ 5/ 9]
ERROR
Please, check the test log
(/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Comp_receptor/9.log)
[INFO ] Alanine Scanning
RUNNING
[ERROR ] Alanine Scanning [ 6/ 9]
ERROR
Please, check the test log
(/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Alanine_scanning/12.log)
[INFO ] Stability calculation
RUNNING
[ERROR ] Stability calculation [ 7/ 9]
ERROR
Please, check the test log
(/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Stability/13.log)
[INFO ] Decomposition Analysis
RUNNING
[ERROR ] Decomposition Analysis [ 8/ 9]
ERROR
Please, check the test log
(/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Decomposition_analysis/14.log)
[INFO ] Interaction Entropy approximation
RUNNING
[ERROR ] Interaction Entropy approximation [ 9/ 9]
ERROR
Please, check the test log
(/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Entropy_calculations/Interaction_Entropy/15.log)
Could anybody help me how to fix error?
I struggle to solve this issue for two days.
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Received on Fri Nov 18 2022 - 16:00:02 PST
