Vishwambhar Bhandare

2 Questions 2 Answers 0 Followers

Questions related from Vishwambhar Bhandare

How to define ligand / metal atoms in gbsa.itp file of a force field for implicit MD??

I want to perform implicit simulation for a protein-ligand complex. for a protein alone, implicit works fine, but for ligand atoms it shows error as copied below, Setting gen_seed to...

03 March 2018 9,923 1 View

How to estimate the statistical error in the fluctuations in Binding energy, RMSF, Rg, SASA. Hbonds etc. ?

I performed simulation of a protein and Protein-RNA complex for a 50ns. I have to interpret all my results RMSD, RMSF, Rg,SASA, binding energy with respect to statistical error. in other...

09 September 2016 4,249 2 View