Sana Saeed

3 Questions 4 Answers 0 Followers

Questions related from Sana Saeed

How to restrain ligand/peptide in Protein pocket for NAMD?

Dear researchers i am following the tutorial http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf but in this tutorial its not mentioned how to restrain ligand in the...

16 October 2016 5,244 3 View

How can I find the lowest energy conformation of Protein-ligand complex after 10 ns simulation?

I have done 10 ns complex simulation for Protein-ligand complex using Gromacs 5.0. the ligand moved out of pocket after 6 ns. Now i want to choose best stable conformation. How can i find the...

08 June 2016 2,920 8 View

Volume corresponding to the one molar standard state in Gromacs?

hi gromacs experts How can i find Volume corresponding to one molar standard state. background i have Protein-ligand complex simulation and i need to find energy of restraints which requires...

21 April 2016 5,303 1 View