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README.org

respac_batch

Description

Simple script to perform RESPAC calculations (including APBS) for coarse-grained protein charge distributions.

Dependency

This package contains only a batch script to easily call pdb2pqr, apbs, surface, and pdcp. The last two are written by Dr. Tsuyoshi Terakawa. Basically, this script is also derived from a Perl version created by Terakawa-san.

UPDATE: Recently Niina-san rewrite the pdcp part, which is faster than the original version. Please ask him for details and download from his git repository.

Run

Simply add the PDB structure file to the pdb_protein directory (“aaa.pdb” for example), and run

./respac.py aaa

where aaa is the file name of the protein.

The output will be a file containing partial charges for surface residues in protein. The file will be stored in the results directory.

Other Tools

There are also some tools to make it easy to convert the output into CafeMol input format, and to plot the distribution of charges. Please see the tools directory.

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Simple script to perform RESPAC calculations (including APBS) for coarse-grained protein charge distributions.

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