Bio-Otto / molmin

Macro-Molecule mutater and minimizer

molmin

Macro-Molecule Mutater and Minimizer

A package for mutating and minimizing

For production just type;

$ python minimizer.py -p <pdb file> -pff <amber96> -wff <tip3p> -mut <ASP-121-ASN> -mut_ch <A>

Also you can check full functional parameters with typing

$ python minimizer.py -h

• -p --> Give the absolute path of your pdb file.
• -pff --> Protein Forcefield (The program defaultly will use amber96 forcefield)
• -wff --> Water Forcefield (The program defaultly will use tip3p forcefield)
• -mut --> The program will apply the mutation described as "target_residue-residue_number-desired_residue" (For example: -mut ASN-120-ASP).
• -mut_ch --> The program will mutate selected residue according to indicated chain ID.

Then run it.

Dependencies

molmin uses a number of open source projects to work properly:

• OpenMM - A high performance toolkit for molecular simulation.
• pdbfixer

And of course molmim v0.1 is open source on GitHub.

The Program applying minimize and mutation according to yur choises using powerfull OpenMM Molecular Dynamic Toolkit, which also supports the Cuda platform.

New Features!

• Mutation
• Fixing non-standart residues
• Minimizing with heterogens or ions

Installation [Not Supporting Yet!]

Open your favorite Terminal and run these commands.

$ cd molmim
$ python setup.py --install

License

MIT

Free Software !