Sushmita Basu

9 Questions 21 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...

04 April 2019 470 8 View

How to succesfully simulate protein-RNA complex in excess salt concentration using gromacs?

I want to simulate a protein-RNA complex in a salt concentration of 150mM. I neutralised the charge of the system by adding 14 Na+ ions and followed that by adding extra salt concentration using...

04 April 2019 1,739 2 View

How to simulate RNA using GROMACS package with amber99sb-ildn forcefield?

I have a modeled structure of RNA with 25 nts. I have renamed the atoms as per the rtp file of the amber99sb-ildn force field. All the steps upto energy minimisation ran without any error. The...

11 November 2018 7,678 3 View

How reliable is a modled RNA structure for further docking and simulation study?

I have a 30 nucleotide long RNA sequence, the binding of which I wanted to study with a protein (which has crystal structure available). I am trying to model the RNA structure and further use it...

08 August 2018 9,457 2 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...

10 October 2017 957 2 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...

11 November 2016 9,033 7 View

Can anyone help me with pepdata package of python, want to use it for amino acid properties?

I have installed the package but cannot understand how to use the functions for amino acid properties for my given set of sequences.

10 October 2015 1,832 3 View

How can i calculate secondary structure propensity of amino acid sequences with values in percentage?

I have 27 sequences of varied length (20-600) for which i need to know the secondary structure propensities.

09 September 2015 4,010 4 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 7,750 4 View