Sana Saeed

10 Questions 8 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...

10 October 2016 6,553 3 View

Anyone using NAMD for simulations?

Hello researchers I am switching from Gromacs to NAMD, i need a little help. if anyone have experience in NAMD please help me. Thanks Regards

08 August 2016 1,142 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...

06 June 2016 887 9 View

What is the standard volume value in free energy of restraint?

i am calculating free energy of restraint for absolute binding free energy system of protein and ligand. i am confused between standard volume values. standard Volume is 1660A^3 , should i use...

05 May 2016 5,531 1 View

Can anyone help me in understanding REMD (Replica exchange Method) protocol in gromacs?

hi Researchers and Scientists i am working on Protein ligand binding free energy, i want to use Replica exchange method for complex simulation as well as ligand in water simulation, i have studied...

05 May 2016 5,486 3 View

Can anyone suggest me the beginner tutorial for calculating protein protein binding free energy using GROMACS?

hi i want to practice protein protein binding free energy calculation MD using Gromacs, i have already done practising protein ligand simulations by using Alchemical pathway. please suggest me...

05 May 2016 5,237 2 View

Is there any rule for selecting atoms for distance restraints?

hi While restraining ligand into protein pocket during complex (ligand+protein) simulation, are we suppose to chose some specific atoms or selection can be random? is there any range of distance...

05 May 2016 1,609 3 View

Free energy of restraints?

Hi everyone, I am trying to calculate binding free energy of a ligand-protein complex. I have done both simulations -ligand in water -protein-ligand complex and calculated both energies, now...

04 April 2016 4,523 0 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...

04 April 2016 3,043 1 View

Can we apply simple solvation free energy calculation simulation for ligand in water simulation in absolute binding free energy calculations?

Hi, all GROMACS specialists. I have a question about ligand simulation in water. In binding free energy calculations of ligand and protein, we need two simulation systems, one -protein+ligand in...

03 March 2016 9,041 5 View