Aashish Bhatt

6 Questions 96 Answers 0 Followers

Questions related from Aashish Bhatt

How to choose enhanced molecular dynamics method to study conformational change in enzyme?

The allosteric mechanism of the enzyme is difficult to get in the nanoseconds range in molecular dynamics simulation. In my enzyme, the allosteric regulator activates the enzyme throughout a large...

22 April 2021 4,044 7 View

How can I convert charmm parameter and toplogy file in to the amber format?

Hi I am following a paper "Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations". In this paper they used charmm force...

26 September 2019 8,258 7 View

How many data points are needed to calculate velocity auto correlation function?

I have performed classical molecular dynamics simulation using NAMD. I want to know IR spectra of some particular stretching mode.

18 March 2019 6,501 5 View

How can calculate elctrostatic potential, charge of protein?

I have been facing problem in generation of charge file or cube file in pdb2pqr server. Can anyone tell me how can i calculate both things? Please help me, I have uploaded charge file screen shot.

07 May 2017 7,382 1 View

How can set a parameter for Ag+ ions in AMBER16?

I have try to simulate a protein with Ag+ ion with ff14SB at AMBER16. When I type in tleap script they showing message vdw parameter is not find. how can I set a parameter for Ag+ ions. please...

23 January 2017 8,030 3 View

How can set parameter for Au+ ion with protein in AMBER16?

I want to use AMBER to calculate Au+ ion interaction with Protein. I have tried to use AMBER force field, but no Au+ parameter in amber force field was found. How can I set parameter for Au + ion...

27 December 2016 9,172 1 View