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,
I could not fix bond length and bond angle of my own choice.
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
Also I find fragbuilder is not that fast in generating peptides.
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.