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Questions related from Maryam Mapar
Hello, about contact map in molecular dynamics simulation. I obtained the contact map of the protein-ligand complex using this command: gmx distance -f md.xtc -s md.tpr -n index.ndx -oall...
29 July 2024 7,788 2 View
I have done docking and molecular dynamics simulation of two wild-type and mutant enzymes with ligands separately. To revise the article, the Reviewer has left this comment to get the contact maps...
25 July 2024 3,976 2 View
In molecular dynamics simulation, to get FEL analysis, I got an error. My Python version is 3.10.7. My input files are made with a lower version of Python. But the final command to generate the...
24 July 2024 6,034 2 View
24 July 2024 2,308 1 View
Hi Can please tell me, To analyze the results of molecular docking and simulation of molecular dynamics (MD) of enzyme and ligand in Gromacs, what other analyzes can be done on them that can be...
20 February 2024 9,632 8 View
Hi Can you please explain to me about the need to do the PCA analysis in molecular dynamics simulation? Thanks alot
10 January 2024 275 4 View
Hi When we want to simulate a metalloenzyme, we must first apply the metal charge using quantum mechanics before performing the molecular dynamics simulation. Now, in this method, the charge of...
10 October 2023 6,645 0 View
I want to use the active site structure of carbonic anhydrase enzyme in my paper. Is it better to draw its structure myself with software such as Discovery Studio or Paymol or...? Or is it better...
20 September 2023 9,661 2 View
When 4-nitrophenylacetate is used as a substrate for carbonic anhydrase 2 enzyme, is there carbon dioxide as a substrate at the same time? thank you
24 June 2023 5,838 4 View
Hi In Molecular dynamics simulation, To test for enzyme stability, We should the enzyme be simulated with and without the substrate. this means that first we must doing Molecular Docking with...
07 November 2021 4,770 5 View
