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Questions related from Sushmita Basu
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 472 8 View
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 1,743 2 View
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 7,681 3 View
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 9,459 2 View
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 959 2 View
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 9,035 7 View
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 1,835 3 View
I have 27 sequences of varied length (20-600) for which i need to know the secondary structure propensities.
09 September 2015 4,013 4 View
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 7,755 4 View