Generating 3D cartesian coordinates of a peptide and computing van der Waal interactions (1-4 atoms) for a given set of dihedral angles?

Question

I wanted to generate 3D Cartesian coordinates of a peptide sequence for fixed bond lengths and bond angles for a given set of backbone dihedral angles and side dihedral angles. I also wanted to compute non-bonded van der Waal interactions (1-4 atoms) for each of the peptide generated from the dihedral angles. I initially tried frag builder module in python although it works fine. There are few issues,

1. I could not fix bond length and bond angle of my own choice.

2. It generates PDB file and save it inside the hard disk. So I need to read it again and parse it to compute non-bonded van der Waal interactions (1-4 atom). It consumes lot of time

3. Also I find fragbuilder is not that fast in generating peptides.

4. Reading , parsing and computing the interactions takes around 30 mins to complete the task for 200,000 3D ensemble of structures of given peptide sequence of length 18.

Kindly suggest me a better module in python which does the job faster and also give reference to it.

Answer 1

The PDB module in Biopython is worth checking out for obtaining angles, distances, torsion angles. It is described from p208 at http://biopython.org/DIST/docs/tutorial/Tutorial.pdf. It doesn't do van der Waal interactions.

For example,

from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.Chain import Chain
from Bio.PDB.internal_coords import *
from Bio.PDB.PICIO import write_PIC, read_PIC, read_PIC_seq
from Bio.PDB.ic_rebuild import write_PDB, IC_duplicate, structure_rebuild_test
from Bio.PDB.SCADIO import write_SCAD
from Bio.PDB.PDBIO import PDBIO

parser = PDBParser(PERMISSIVE=1)
myProtein = parser.get_structure("1a8o", "1A8O.pdb")
myChain = myProtein[0]["A"]
IC_Chain.MaxPeptideBond = 4.0
myChain.internal_coord = None
myChain.atom_to_internal_coordinates(verbose=True)
r2 = myChain.child_list[1]
r2ic = r2.internal_coord
r2chi1 = r2ic.get_angle("chi1")