Jesus David Castaño

4 Questions 3 Answers 0 Followers

Questions related from Jesus David Castaño

How to do Molecular Dynamics with Flexible docking tools (ADFR & Gromacs)?

Hi all, I'm trying to use AutoDock Flexible Receptor (ADFR) to do a flexible docking between a membrane protein and its ligand. I already got some candidate poses, and I'd like to validate them...

22 January 2025 1,277 3 View

How to plot 3d surfaces from MD simulations with Gromacs?

Hi all, I'm trying to plot Free Energy Landscapes from Gromacs after using the gmx sham function. After using the command: gmx sham -f PCAplot2d.xvg -notime -ls gibbs1-2.xpm (where...

08 July 2020 1,378 1 View

Why I am getting additional bands in PCR after extracting plasmid from transformants and using M13 primers?

Hi, I have been trying to amplify a segment containing my gene of interest in the TOPO TA vector pCR2.1 using the sequencing primers M13 and M13(-20). However, it seems that I am getting some...

22 March 2019 3,459 3 View

How I can include metal ions in a enzyme when I am using modeller?

I am relatively new at bioinformatics, and I am trying to model an enzyme for docking analysis. I have used modeller, but the template of my enzyme does not include de metal atoms that I know are...

05 October 2015 4,732 3 View