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Questions related from Brandon Havranek
Hello, How do you all normally analyze multiple MD simulation trajectories. For my system, I ran 5 100 ns simulations using an different initial velocity. Do you perform cluster analysis and then...
10 March 2022 7,023 3 View
Does anyone have experience using the AlaScan plugin in VMD to make FEP simulation files for alanine scanning? I keep trying to create the files but I am getting a number of errors: I even used...
12 August 2021 4,972 4 View
Hello, I am looking to calculate the binding free energy between two proteins. I am looking for the most widely accepted and rigorous method. I was thinking about using FEP. However, I noticed...
30 April 2021 3,430 3 View
I ran ligand docking and I created a ligand-protein complex PDB in Chimera. Both the ligand and protein are saved and when I open the PDB I can see both structures together. However, I am trying...
12 March 2020 1,852 4 View
Hey all, I am using the PyRx version (.8 and earlier free version). I am looking to do virtual screening of 2000+ ligands to my target molecule. I have all molecules in a sdf format inside a...
23 February 2020 7,039 3 View
Hello all, I have a few designs that were constructed computationally using Rosetta. Almost all papers using Rosetta design use high-throughout yeast display, encoding the designs in oligo...
01 January 1970 5,376 1 View
Hello all, The charmm-gui absolute ligand binder (https://www.charmm-gui.org/?doc=input/afes.abinding) creates files for running FEP/λREMD simulations using NAMD. The default settings employs 32...
01 January 1970 7,580 1 View
