Tanusree Mookherjee

5 Questions 8 Answers 0 Followers

Questions related from Tanusree Mookherjee

I want to simulate a protein- Phosphatidic acid complex in gromacs but cant generate the topology for phosphatidic acid,?

I am having an issue regarding Phosphatidic acid topology generation for Gromacs 5.1.5 simulation. I would like to study the protein-ligand dynamics. Kindly help

04 June 2023 7,747 5 View

How to simulate protein-phosphorylated protein complex in presnece of zinc in gromacs 5?

I have a phosphorylated protein ligand docked to my protein receptor, i would like to simulate the structure , but after adding forcefield using charmM , an error is occuring saying- "T2P not...

26 April 2023 423 6 View

How to start a mD simulation of a protein docked with a phophorylated protein lignd using Groamcs?

one kinase and its scaffold protein in a phosphorylated version is needed to be simulated. How to standardizes that and what water model shall i use?

25 March 2023 1,171 0 View

Why my RMSD graph of two helical heterodimeric proteins is getting distorted?

The molecular simulation of two 50 amino acid long helical proteins forming heterodimer has ran 100ns then again ran for 50 ns. But the RMSD graph deformed. I have used gromacs 5.0 and saved it...

20 June 2019 6,940 7 View

How to do gromacs simulation in a remote machine”

How to perform gromacs on a remote machine for proteins longer than 500 amino acids for atleats 120ns

01 January 1970 4,298 8 View