Vishnu Kumar Sharma

4 Questions 4 Answers 0 Followers

Questions related from Vishnu Kumar Sharma

How to prepare a ligand in amber which is covalently bond with protein?

I am trying to perform MD simulations in Amber for a protein-ligand complex (PDB id: 5YY1). The ligand is covalently attached to a side chain atom of an amino acid (for example: ----EDSKL---- a...

19 September 2019 6,434 3 View

How MMGBSA from prime module of schrodinger is differ from AMBER MMGBSA?

I performed MMGBSA from prime module of Schrodinger which took 2 to 5 minute for calculation while MMGBSA from AMBER taking 3 to 5 hrs approximately. Why?

27 June 2018 839 4 View

How to generate virtual chemical library, If I have a Head group, linker and tail group?

I have to generate a virtual library. I have 10 different Scaffold or Head group, 10 different linkers to connect with Head group and 10 different Tail groups which can attach with linker on...

08 February 2017 9,094 2 View

Basic requirements to go for ligand based pharmacophore design?

Hi, I am to go for ligand based pharmacophore design, before going to start I need some basic knowledge about pharmacophore design like ligand based vs structure based, preliminary requirements or...

28 October 2015 7,865 3 View