allenpark96 / pdb4amber

PDB analyzer and fixer for Amber simulations

Install

• Require

  • ParmEd
  • tleap (optional, used for build structure, add missing atoms, mutation, ...)
  • scipy (optional, used for minimization)

• Quick install

From AmberTools

conda install ambertools -c conda-forge

Or directly from github

pip install git+https://github.com/amber-md/pdb4amber

Usage

$ pdb4amber --help

# Some examples
# simplest case, print output pdb
pdb4amber my.pdb 

# simplest case, save output to file
pdb4amber my.pdb -o out.pdb

# compat mode
pdb4amber -i my.pdb -o out.pdb

# pipe
cat my.pdb | pdb4amber -o out.pdb

# save to different formats (e.g: mol2)
pdb4amber my.pdb -o out.mol2

# use `reduce` program to add hydgron
pdb4amber my.pdb --reduce -o out.pdb

# process other formats (e.g: .cif)
pdb4amber my.cif --reduce -o out.pdb

# process from URL
pdb4amber https://raw.githubusercontent.com/ParmEd/ParmEd/master/test/files/4LZT.cif -o out.pdb

# fetch structure by its pdbid and process
pdb4amber 1tsu --pdbid --reduce -o out.pdb

# logfile
pdb4amber my.pdb -o out.pdb --logfile=my.log
pdb4amber my.pdb -o out.pdb --logfile=stdout

Test

py.test -vs .

Pull to amber repo

• It's a submodule in amber git.