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Questions related from Bruno Santos
Hello everyone, I am working on a peptide-protein interaction simulation and I want to extract the RMSD of the interaction as suggested by mdtutorials. Specifically, I need to calculate the RMSD...
27 November 2024 3,061 2 View
I still find Packmol very tricky with parameters. I have two pdb files, one with a pre-quilibrated bilayer and one with the peptide of interest. How can I create a system with three copies of the...
30 April 2024 8,319 1 View
I am trying to calculate how many SDS molecules I need in a MD box to achieve a specific concentration (ex: 1M). My first doubt is if I use the box volume or the quantity of water molecules, for...
17 April 2024 2,160 2 View
The 1956 paper A simple ultraviolet spectrophotometric method for the determination of protein is constantly referenced as the one who provided a method for peptide concentration calculation that...
09 June 2023 973 2 View
I am trying to implement a REX simulation on gromacs to analyze my peptide's folding, and the work of Kubitzki and de Groot (2008) has called my attention to TEE-REX simulation. Peharps the...
13 December 2022 3,867 0 View
I'd like to put the peptide molecule on the surface of a membrane, instead of inside, to observe affinity and capacity of trespassing the bilayer barrier. How can I do that on GROMACS?
06 June 2019 2,383 4 View
I work with peptide-bilayer interactions and I have tried a few strategies to observe the partitioning and folding of peptides, however without good results. If the problem is sampling, Replica...
01 January 1970 3,789 7 View
Hi, I’ve recently started investigating receptor-ligand interactions using peptides as ligands. My approach involves docking to determine the initial binding pose, followed by molecular dynamics...
01 January 1970 2,219 2 View
