Marco Carnaroli

6 Questions 12 Answers 0 Followers

Questions related from Marco Carnaroli

Why are metal ions running away from the protein active site durinng an MD simulation?

Hello everyone. I'm currently facing the following problem: I'm doing with Amber MD simulations on a protein that has metals ions (zinc and copper) in it to perform its biological activity and to...

25 August 2024 1,764 5 View

Is it normal for the RMSF to be so different?

Hello, I performed with Amber three replicas of a 1200 ns MD simulation on a protein dimer (wild type one), using the exact same parameters (except for the random seed that changes the initial...

10 August 2024 8,223 2 View

How to create parameter and coordinate files for ligand in amber when FATAL error (maybe due to duplicate bond specifications) happens?

Hello, I'm trying to create parameter and coordinate files for a drug (PRG-A01) found on the following page: http://www.probechem.com/products_PRG-A01.html I used the guide made by Michael...

18 July 2024 3,757 3 View

What should be done when molecular dynamics simulation replicas yield significantly divergent results?

Hello. Currently I'm doing 300 ns MD simulations in Amber to look for differences between a wild type protein and mutated ones. In detail I have one wild type dimer and 7 mutated dimers. So I...

15 July 2024 3,512 11 View

Is possible to dock metals (metal ions) with an apo-protein using MOE?

Hello I need to perform a docking between some metal ions and a protein, in order to study the stability of that protein before and after the metalation. Which software can be used to achieve that...

09 May 2024 3,392 4 View

Why does Amber return this syntax error?

Hello, I'm quite new here. I'm just following a tutorial based on the folding Trp Cage Amber tutorial. When I try to do the minimization with the following code: pmemd -O -i 1min.in -o 1min.out...

09 May 2024 7,749 2 View