Hello all, I'm a bioinformatics researcher and trainer, specialising in Structural Bioinformatics area and running a bioinformatics training and consultancy startup.. Hoping to share and exchange bioinformatics knowledge with world community..
Sit how you doing this so fast , its takes almost a month in my system to complete one simulation!!!! My md run takes 12 hrs for nvt and npt and md production take one month!!!also i have gpu support!!Can you help me please
That's strange. Could you please specify your computer and MD system configuration? Like which cpu, gpu and ram and also how big is your protein.. I also suspect that gromacs is probably not using GPU else it wouldn't be that slow.. your can check that with command gmx --version --quiet to check which cuda it's using our not using.. or while running the MD you can check with command nvidia-smi whether or not GPU is being used
Can we use batch mode for multiple ligand simultaneous docking? For example, I want to keep ligand 1 common and the ligand 2 to change in each docking, can we perform such docking using batch mode? Any assistance in this regard will be very helpful. Thank you.
The command that ordered to calculate rmsd between ligand and protein by vmd in tutorial is protein or resname K23 is that true Please anyone correct me
Sir is it safe to run GROMACS in laptop.. I have a HP Omen gaming laptop. Can I use it for simulation? or running simulations will affect its hardware?
It is safe to do so but always make sure while simulation is running, your laptop is around a good ventilation or under a fan or AC as it gets heated up running for several days.. typically for small simulations, it's not at all a problem to run on laptop.. it won't affect the hardware
Sir I have seen your LinkedIn profile and sent you a connection request. Sir I want to study Bioinformatics master's from abroad and for my SOP I want to know that what specialisation of bioinformatics (out of genomics, proteomics and biomarker analysis is used in treatment of autoimmune diseases like multiple sclerosis). I have studied Bsc. Life sciences and do not have much knowledge regarding bioinformatics that's why I want some expert's advice.
hello, I have one queries if there is no X-RAY structure present for certain protein, can we take Electron Microscope(EM) Structure greater than 3 armstrong resolution for docking
Yes, EM structure can be used but it is advisable to run a good amount of energy minimization on the structure using good minimization program or MD. If structure is very flexible overall, you can create multiple confomers from MD and perform docking against each of the top conformers of the protein
Hello! Thank you for this very informative video. I was wondering if converting SMILES format to the PDB format would make a difference in terms of docking ligands. Thank you in advance.
Hi, not really. It's a very standard to convert SMILES into a sructure format. But before converting to PDB directly, It's better to convert to more suitable format for small molecules like SDF or MOL or MOL2 and making sure you are optimizing the geometry of molecules by energy minimization so PDB can be a reasonable connected structure.
It really depends on the PDB organization. In most common cases, if the PDB consisting of multiple identical chains of the same protein, you can delete any of the chains and use one. But if PDB consists of various proteins or subunits, you need be sure which protein or domain you are inerested in targetting. If this information is unavailable, you can try docking all chains/pockets to find the suitable one.
What are Gasteiger and Kollman charges? Where exactly are these charges being added in the protein? How can I determine the location of these charges in the protein
If the gromacs has been compiled with GPU during installation, but default, mdrun launches the run on both CPU and GPU so no extra steps are necessary. Nevertheless, to specify number cores or GPU or the tasks that need to be offloaded to GPU can be set by various parameters like -nt for number of cpu threads , -gpu_id to specify a gpu, -nb gpu to offload non-bonded calculations to GPU.. etc
Yes you can. But cryo-em structures are low resolution, hence to generate good atom level coordinates, it's useful to process the cryo-em structures with energy minimisation or small molecular dynamics simulation before using it for docking
Hi, I am really impressed your video. I have a question. Your first video you used a UCSF Chimera and AutoDock vina, and in this video, you use AutoDock Tools with AutoDock vina. AutoDock Tools can be replaced with UCSF Chimera? Do they perform similarly?
Hi, yes for simple docking purposes, AutoDock tools can be used instead of Chimera to generate the PDBQT files, but Chimera does have some additional capabilities which are not present in AutoDockTools like filling up missing atoms from side chains, protonation states of residues etc.
Thank uuuuuu so much, sir... But one request sir. I'm a BS student of microbiology so I want to do an ms and PhD in bioinformatics. So I need more tutorials about the bioinformatics course and also the practical section too with each topic. Thanks once again 🤲
Nice explaination. I have obtained dipole moment of a molecule using gromacs, but how I can visualize it in vmd as a vector along with my molecule. Should i give this dipole.xvg file as an input to vmd???
Hi dear Please I need to ask you about dipole moment What is important to calculate it in MD simulation process What is the idea that I get form dipole moment value ?? Thank you dear
my protein have zinc ion and hydroxide ion. i tried all type of forcefield but i could not run simulation it shows error zn residues not found or oh residue not found. did you have any suggestion for run my protein.
