Sandali L.

6 Questions 7 Answers 0 Followers

Questions related from Sandali L.

Which is more suitable for MD simulation of CHARMM-GUI generated files under CHARMM-36 FF? NAMD, AMBER or GROMACS?

I have prepared the simulation files for a protein-membrane system using CHARMM-GUI membrane builder option. The force field used there is CHARMM36 FF. Can you please tell me which MD simulation...

20 June 2022 1,282 2 View

Does a GPU cluster need to run a MD simulation of protein-membrane system for 10ns?

I'm working on a protein-membrane system where I have to run a MD simulation of 10ns repeatedly. I'm currently using a CPU cluster but my equilibration steps get interrupted without completing the...

15 June 2022 3,022 0 View

Are Swiss model structures accurate for homology modeling?

In a study, I have to do a comparison between the existing homology models in the literature and the AlphaFold structure by running MD simulations. But only the available homology model is built...

13 June 2022 1,079 2 View

How to build a complete homology model of receptor without having a template which covers the N terminal domain?

I don't have any template which covers the n terminal of the query sequence all the homology models which I am intending to build are missing the n terminal domain. What would be the best option...

13 June 2022 5,989 1 View

Why .xtc file has not generated in a production md?

I have run the production step for a protein-membrane system using Gromacs. But, the relevant stepX.X_production.xtc has not generated so that I can't proceed to the RMSD analysis. How can I fix...

31 May 2022 7,701 3 View

How to model N-terminal residues of a GPCR?

I'm currently working on a GPCR and I need to model its N-terminal residues which are missing in its PDB structure. I need to have the correctly modeled N-terminus because I need to check its...

04 March 2022 2,967 4 View