Marlet Martínez-Archundia

3 Questions 7 Answers 0 Followers

Questions related from Marlet Martínez-Archundia

How can we interpret the thermodynamic terms from CaFE Software?

We have used CaFE Software to predict the binding free energy of our protein-ligand complexes from our molecular dynamics simulations. Fortunately the Software has run successfully however don’t...

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Mebrane protein simulation (NAMD)

I tried to run a MD simulation of a membrane protein. I have followed the Tutorial for Membrane Proteins (NAMD), using CHARMM36 force fields and a POPC lipid bilayer to embed my protein. However...

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How to wrap a protein correctly using VMD and save a new dcd?

Dear all, I have been trying to "wrap" my protein in the trajectory using the following command, using VMD: set sel [atomselect top protein] pbc wrap -centersel $sel origin -compound res -all. I...

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