Robertson Rivera

7 Questions 15 Answers 0 Followers

Questions related from Robertson Rivera

How to go about problems launching autodock tools 1.5.6 and 1.5.7?

I'm a windows 11 user and I am having problems launching autodock tools 1.5.6 and 1.5.7. The GUI will just launch up to 6-8% and then it will crash and will not continue opening. I already tried...

28 April 2023 1,401 4 View

Redocking in Autodock Vina can I choose any of the conformation as long as its RMSD compared to the original cocrystallized ligand is less than 2?

Hi, I have been trying to redock the cocrystallized ligand of the PPARG protein with PDB ID 4yt1. The best conformation (best binding energy) has a high RMSD relative to the original...

01 August 2022 4,239 6 View

Reporting binding energies (kcal/mol) obtained using Autodock Vina?

I would like to ask if I can report the values of binding energies obtained using autodock Vina as mean +/- standard deviation? I docked the ligands in the receptor 5 times (5 trials). Thank you!

11 November 2021 3,916 3 View

How to compile all log files in 1 text file and extract certain information for easy transfer to excel sheet?

Hi, I'm doing molecular docking using autodock vina. The output file is *.log and there are thousands of them. I would like to know how can I compile all the log files in 1 and extract the...

29 October 2021 6,997 3 View

Batch Ligand Preparation on Autodock Vina?

Hi, I'm trying to dock thousands of compounds using autodock vina. I already have the script for running the compounds without manually docking them one by one on the GUI of autodock tools....

27 October 2021 1,492 4 View

Is there a software than can do both protein-ligand and protein-protein docking?

My selected target has an antibody as its ligand. However, my compounds of interest are not proteins/peptides so I'm having difficulty in solving this problem because I cannot use two different...

18 September 2021 9,151 15 View

How do you convert the CASTp3.0 output into XYZ coordinates in autodock tools to set up gridbox?

Hi I'm doing a molecular docking simulation and I would like to know how to convert the output of CASTp3.0 (Volume, Area, amino acid residues) into the XYZ coordinates of the grid box in autodock...

15 September 2021 1,828 1 View