Alvea Tasneem

7 Questions 12 Answers 0 Followers

Questions related from Alvea Tasneem

How can I calculate the Boltzmann Weighted average for thermodynamic properties?

Hello, Is there a way to calculate the Boltzmann weighted average of thermodynamic properties calculated using the hsa_gist command of the SSTMap tool? thank you

12 March 2023 8,800 1 View

Any tool on how to calculate grid inhomogenous solvation theory for hydration site in MD simulated structures?

Hi, Are there any freely available tools/software to calculate GIST? especially for Charmm, NAMD, Gromacs input files... Thank you.

15 January 2023 6,092 0 View

How can I download natural compounds from ZINC15/ZINC20 database?

Hello, I want to download all the natural compounds from ZINC15 or ZINC20 database (either smi, sdf, or mol2 files). https://zinc15.docking.org/substances/?page=1...

03 January 2023 8,190 9 View

How to prepare alphafold predicted protein structure as receptor for virtual screening and molecular docking?

Hello everyone! I have an anti-viral drug target structure with 1087 amino acid residues which are predicted by alphafold. I wanted to know how can I prepare this alphafold predicted protein...

01 September 2022 7,477 11 View

Is there any TCL script program to identify specific MD water molecules forming hbond with certain residues in every frame upon selection?

Hello, I need to check which water molecules (MD simulations) with their specific water IDs are coming at the catalytic pocket of my protein within hydrogen bond distance in 500 frames, i.e., in...

31 January 2022 8,757 2 View

How to minimize the standard deviation of protein-ligand complex using mmpbsa (CaFe 2.0 vmd plugin) using namd?

Hello, I wanted to know how can I minimize the standard deviation (SD) of my simulated protein-ligand complex of 50ns using MM/PBSA method of Cafe 2.0 plugin of VMD plugin using NAMD. I have tried...

11 December 2020 8,271 1 View

What is the configuration file for blind docking using PyRx for multiple ligands?

I am trying to run blind docking with multiple ligands and one macromolecule using PyRx but somehow i am getting poor binding affinities. What is the configuration file for blind docking in PyRx...

02 April 2019 2,254 3 View