Arun Bahadur Gurung

3 Questions 5 Answers 0 Followers

Questions related from Arun Bahadur Gurung

How to get parameters for Platinum atom types in AutoDock version 4.0?

Dear All, The ligand which we have selected for our docking studies contain a Platinum atom, whose parameters need to be defined prior to docking. In this regard, could you please suggest a way to...

11 November 2016 6,189 3 View

How to extract different meta-stable conformations from free energy landscape (FEL)?

Dear all, I have generated free energy landscape (FEL) plot by projecting Principal component 1 (PC1) and PC2 using g_sham program of GROMACS vs 4.6. But, I failed to understand how to extract the...

10 October 2016 9,423 2 View

How to keep the two strands of DNA together during MD simulation?

Dear All, I performed MD simulation for DNA-ligand complex for 20 ns using GROMACS v.4.6.5. with AMBER 99SB force field. The ligand topology was obtained using AmberTools 14. The results of RMSD...

01 January 2016 6,641 3 View