Tomek Stępniewski

4 Questions 6 Answers 0 Followers

Questions related from Tomek Stępniewski

Is it ok to simulate protein ligand interractions using Coarse Grained forcefields?

Hi, I would like to study how a large protein complex interracts with a ligand. Due to the sheer size im afraid im limited to Coarse Grained. Im guite confident about the protein, however the...

01 January 2019 1,254 3 View

Why define the "steps per cycle" value, when you could just use the timesteps in NAMD?

Hi, I have very general and basic questions considering NAMD. In the input you define timesteps, but you also define steps per cycle. If I understand correctly, atoms will be moved to another...

10 October 2014 6,250 4 View

Can anyone help me solve a problem with contact residues in binding pockets?

Hi, I've just started screening experiments to determine the molecular binding mode of four proteins, and unfortunatelly I still have problems determining which sidechains are in contact with the...

07 July 2014 4,241 10 View

Does anyone know a solution for when NAMD adds bonds between my membrane and protein?

I'm currently working on membrane protein dockings, and I'm trying to prepare a file for molecular dynamics in NAMD, unfortunatelly after i try to combine the protein and membrane files, VMD...

03 March 2014 8,173 3 View