Shakir Ali Siddiqui

4 Questions 3 Answers 0 Followers

Questions related from Shakir Ali Siddiqui

Can anyone help me in finding the x-ray crystal structure database for the Covalent Organic Molecular Cages?

Hi, Just like, there exists an x-ray crystal structure database RCSB protein data bank for proteins & enzymes and Cambridge crystallographic data center for finding metal-organic framework...

23 July 2021 5,791 3 View

How to calculate the acceleration/velocity of different molecules in an MD Simulation?

Hi, If I am performing an MD Simulation in which the two groups/molecules are moving in a direction on applying a force on the system, how would I calculate the velocities/acceleration of the two?...

09 February 2021 9,664 4 View

Can anyone please help me using polarizable force fieild in Amber18?

I am using force field ff02 and water model POL3. I am having difficulty in minimizing the system. In the Minimization output file after 100 steps of minimization EPOLAR = ************ EEL =...

18 December 2020 506 3 View

Is there anyone who can help me parameterizing theligand molecule with AMOEBA polarizing force field for using it in AMBER?

I am able to generate the parameter topology files for protein and water box using TINKER but am not able to generate these for my ligand as it is finding no atom types and atom class in TINKER....

18 December 2020 4,431 1 View