7 Questions 11 Answers 0 Followers
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...
25 April 2019 1,758 7 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...
13 October 2017 9,853 3 View
I have solvent accessibility values for residues in specific positions for a number of proteins. I do not understand how can i represent the data by which i can show that there is a periodicity in...
18 July 2017 6,921 3 View
I have a list of phi, psi angles derived from a number of PDB files based on some criteria. I have plotted a scatter plot using matplotlib with them. But i want to show the favoured, allowed and...
18 July 2017 1,811 5 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...
30 November 2016 8,450 6 View
I have run a simulation for 300 ns. Now i want to extend it upto 1500ns. if i run the input.production.conf file will it run again from the beginning or shall take up after 300ns? if it would take...
30 November 2016 8,787 2 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 9,186 3 View
