Zahra Aliakbar Tehrani

5 Questions 11 Answers 0 Followers

Questions related from Zahra Aliakbar Tehrani

How to set orientation of membranes domain for implicit solvent model in CHARMM?

Dear all, Hi. I would like to do simulation for my full protein model (including transmembrane domain) extracted from Cryo-EM reported pdb file. I have used Orientations of Proteins in Membranes...

26 March 2020 8,688 0 View

How calculate dynamic cross correlation map in AMBER with CPPTRAJ?

Hi all, I would like to do dynamic cross correlation map analysis with AMBER for the ligand and some selected residues/waters around the ligand it in the pocket. I am wondering how to set...

01 August 2019 6,669 6 View

How to move the protein in the center of created water box in packmol?

Drear all, I would like to make water-box/ions for my protein-complex system. Could make it with automated feature in packmol: solvate.tcl structure.pdb -shell 15. -charge +5 -density 1.0 -i...

23 July 2019 2,513 1 View

How to use NAMD energy plugin for interaction energy of ligand-selected residues on AMBER-MD results.?

Hi all, Hi all, I have done md simulation for my system (ligand-protein complex) with AMBER16 and I would like to do some EDA analysis on it using NAMD energy plugin in VMD. I have tested it...

04 July 2019 1,015 3 View

How to wrap protein (dimer)-ligand complex with CPPTRAJ in AMBER?

Dear all I have done multiple trajectories MD (100 ns in total or 5*20 ns) for my system with AMBER16. The Protein-ligand complex are mostly located in the edge of the water box during simulation...

30 June 2019 9,915 8 View