My name is Dr Hafiz Muzzammel Rehman. I'm Assistant Professor at University of the Punjab.I have been teaching Biology and Chemistry since 2006.Im also a columnist at Daily Jang Newspaper. I have been working as Forensic Scientist in Punjab Forensic Science Agency as Crime Scene Investigation expert, Fire scene expert etc. I'm also trainer in Drug Designing & Discovery , Vaccine Designing , Bioinformatics and Chemoinformatics etc
I'm here to explore the advance knowledge about Biology , Chemistry and in the field of Drug Designing and Discovery , vaccine designing etc free of cost to support those students who can not afford expensive fee for getting such sort of education. You can email me at Muzzammel.phd.ibb@pu.edu.pk
Dear Dr you shared a very valuable tool to do simulation but could you please let me know why some commands are not working should we buy access of LGPU or what ?
Hi sir .. thank you for the helpful description... can you please help to perform docking of ligands-metalloprotein (protein with metal ions as co-factors in receptor) using autodock?
Hello Dr. Rehman, Thanks for the insightful video. Please I am Mohammed from Ghana. I am using AutoDock Tools, AutoDock Vina and DS visualizer. When I do the docking, the ligand breaks at the rotatable bonds of the ligand. This makes it difficult for me to calculate RMSD and only one section of the ligand shows in the 2D diagram viewed by 2D visualizer. Please is there anything I am missing. Thank you.
Thank you Dr Muzammel Rahman for the comprehensive tutorial on MD using GROMACS. I have gone through the tutorial till the end and it was very helpful, indeed. One thing I noticed at the end is, that you forgot to combine the two commands together i.e., printf "proteins" | gmx xxxx x x x x x x xx x x xxx.. You just forgot to add " | " to your code. If you had added this the code would have worked correctly. Anyhow, the session was nice and I understood many things from this tutorial. Great work.
Buy minimise option or equilibration and the production steps If by equilibration and the production steps which frame will be the minimise structure? Thank you for your answer dear Doctor
very informative. I predicted 3D protein structure using Phyre2, then got a model with 99% confidence, and 18 % coverage. 58 % of residues are disordered. May I use this protein for docking analysis?
Im performing docking on a known active site so i limited the gridbox around the active site only. Some of the conformations i got after docking were outside the grid box. Is that normal?
Hello professor , thank you so much for you explanation, i wanna ask you if the pdb file of the complexe generated with cb dock can be submitted to MD simulation without any problems?
@@MuzzammelRehman but how to import local files? i tried uploading the file even through drive.... in your provided tutorial i aam facing issue at the downloading steps even i have changed the links..
Hi,doctor such a great lecture 👌 with fantastic explanation and exclusive work work. Allaha bless you Wishing you sucess and cooprate with you in work❤🎉🎉🎉😊
