marktoakley / peptidenanotubes Goto Github PK

Software to construct and analyse cyclic peptide nanotubes.

This program constructs Amber input files containing cyclic peptide nanotubes.

These programs count parallel and antiparallel hydrogen bonds in the structures of cyclic peptide nanotubes. The hydrogen bonds are defined using the DSSP method. The input structures can come from PDB files or PATHSAMPLE databases

Tubemaker depends on the numpy python library. It also requires an Amber library file (several are available in AmberTools, which can be obtained from the Amber website).

To build these programs you will need a fortran compiler (I use gfortran). Build with:

cd src
make

Tubemaker constructs an Amber inpcrd file containing a cyclic peptide nanotube. Run Tubemaker with:

python nanotube.py <#rings> <#residues> <res_name> [arguments]

For example, build an antiparallel tetramer of cyclic octa-alanine with

python nanotube.py 4 8 ALA --anti

The initial coordinates for the peptides are taken from an Amber library file. By default, the ff03 library from Amber or Ambertools is used (if one of them is installed). Otherwise, a library file can be specified with the --lib argument. For a full list of arguments, use:

python nanotube.py -h

Analyses the hydrogen bonding pattern in a PDB file. Usage:

PDBHbond <string file> <int residues> <int rings>

The arguments are the name of a PDB file, the number of residues per ring and the number of cyclic peptide rings. An example PDB file is in the examples directory.

Analyses the hydrogen bonding pattern in a PATHSAMPLE database. Usage:

PSHBond <int residues> <int rings> <int res_size>

The arguments are the number of residues per ring, the number of residues per ring and the number of atoms per residue. For example, the cyclo-Ala8 dimer:

PSHbond 8 2 10

Currently, only cyclic peptides containing one type of residue are supported (but d- and l- variants of the same residue are fine). This program writes a file called hbonds.csv containing properties of the cyclic peptide nanotube.

If you use this software, please cite:

Mark T. Oakley and Roy L. Johnston, J. Chem. Theory Comput., 2014, 10, 1810-1816. http://dx.doi.org/10.1021/ct500004k