Sushmita Basu

4 Questions 9 Answers 0 Followers

Questions related from Sushmita Basu

How to determine the box dimension for umbrella sampling?

I am using Gromacs 2016 to do umbrella sampling of a protein-RNA complex. I am following the Lemkul's tutorial of umbrella sampling, but I couldn't get how the box dimension was determined. For a...

25 April 2019 1,616 7 View

How to seggregate RNA bound proteins from a list of pdb files?

I have a dataset of pdb files which are all complex structures. From them, I have to select only those which are protein-RNA complexes. I code in python. I am trying to use a keyword or pattern to...

13 October 2017 9,722 3 View

What is the preffered force field for an idp-RNA complex simulation?

For protein-RNA complex, amber ff14SB works good, but am not sure if this forcefield will be ok to use for a disordered protein complex. Pl. suggest the optimum choice of forcefield and the...

30 November 2016 8,320 6 View

How to find if a pdb file is having complex structure or unbound structure?

I have a set of pdb files which I have to seggregate into monomer, dimer (homo+hetero) and protein-nucleic acid. Kindly help with the keyword to look for, I shall write my code accordingly. Thanks...

01 January 1970 9,058 3 View