Bharat Gupta

4 Questions 11 Answers 0 Followers

Questions related from Bharat Gupta

Umbrella Sampling using Amber ?

Hi, I am studying a simultaneous proton transfer, bond breakage and nucleophilic attack (by water molecule), using US approach for which I had already performed 5ns QM/MM simulation. All three...

07 July 2016 1,026 4 View

How to calculate structural entropy for certain conformation in MSA?

I have an MSA of homologous sequences of beta-turn for which I have calculated the turn type (I'/II'/I/II). Now to quantify in terms of a score for the conservation of turn types, which...

02 February 2014 8,533 1 View

Anyone have experience with Replica Exchange Molecular Dynamics (REMD)?

I have posted this query in a Gromacs forum, but got no reply. Can anybody give an advice on the following question? I am trying to apply the REMD to study the difference between the folding...

02 February 2014 6,003 13 View

Evolutionary Conservation of Motifs in Protein Structures?

I am interested in studying the evolution of a certain motif in homologous proteins. Actually, I generated a set of non-homologous proteins to study the conservation of the same motif and found...

02 February 2014 8,641 5 View