MCCE Program Run and Debug

Commands and Tools

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getpdb

Command line tool to download pdb file from PDB

Author: Yanjun Wang

Syntax:

getpdb pdbID [file]

This program gets a pdb file from Protein Data Bank, and saves to a file with its PDB name or a user named file.

Example:

getpdb 1akk
Download with url https://files.rcsb.org/download/1akk.pdb.
Download completed.

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vdw_pw.py

Update Lennard-Jones potential of step 3 in files head3.lst and energies/*.opp

Author: Junjun Mao

Syntax:

vdw_pw.py

This program updates Lennard-Jones potential of step 3 in files head3.lst (vdw0 and vdw 1) and energies/*.opp (vdw column). It corrects the some parameter issues in mcce step 3 and offers a chance to rerun vdw calculation without running PB solver again. Also it checks the possible inconsistancy in parameter files and comes with two other tools: vdw_conf2conf.py and vdw_bk.py to inspect the vdw interaction clashes.

Example:

vdw_pw.py