How to Install and Uninstall pdb2pqr Package on Ubuntu 21.10 (Impish Indri)

Last updated: May 04,2024

1. Install "pdb2pqr" package

This tutorial shows how to install pdb2pqr on Ubuntu 21.10 (Impish Indri)


    
        
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                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                pdb2pqr
            
                    
    
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2. Uninstall "pdb2pqr" package

Please follow the guidance below to uninstall pdb2pqr on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                pdb2pqr
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the pdb2pqr package on Ubuntu 21.10 (Impish Indri)

Package: pdb2pqr
Architecture: amd64
Version: 2.1.1+dfsg-7build1
Priority: optional
Section: universe/science
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 2891
Provides: propka
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2), python3 (<< 3.10), python3 (>= 3.9~), python3:any, python3-numpy, python3-networkx
Suggests: apbs
Replaces: propka
Enhances: autodocktools
Filename: pool/universe/p/pdb2pqr/pdb2pqr_2.1.1+dfsg-7build1_amd64.deb
Size: 385468
MD5sum: b977d5c54aaffb856ccde3ec86ea49b8
SHA1: aa2c3141643fd36e7dad7e7d4008e18075aa7e07
SHA256: 802606a6972cafe0f57ef284db4ef3b1a5254f188c49d3f4eb28c2d14b701dbf
SHA512: 5b04f4bf6a93e37227d3f7ed72a5ef0805d8e6ad11ebb3909559015a13496de68bc14bb091b4568583366b8b731494138fa8705d23e9e13924306375df4990cf
Homepage: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
Description-en: Preparation of protein structures for electrostatics calculations
PDB2PQR is a Python software package that automates many of the common
tasks of preparing structures for continuum electrostatics calculations.
It thus provides a platform-independent utility for converting protein files
in PDB format to PQR format. These tasks include:
* Adding a limited number of missing heavy atoms to biomolecular structures
* Determining side-chain pKas
* Placing missing hydrogens
* Optimizing the protein for favorable hydrogen bonding
* Assigning charge and radius parameters from a variety of force fields
.
This package also includes PropKa, a tool to modify the protonation state of
protein structures in the Protein Data Bank (PDB) format to match a given pKa
value. It can also be used to refine NMR structures, which often yield
inaccurate pKa values for some residues.
Description-md5: c9a453086cb5c3679e524923f0e977d2