Is it fine to obtain 3d structure from pubchem already

Aye man, ain’t nothing about no journey inside me 🙅‍♂️

the lady voice was very very unclear sadly but video worth watching

I'm drinking water. I love you water. You're my life, literally

Sir, I got an error of unknown atom as Si, how can I solve, pls any one help

So if you’re perfectly hydrated and consuming the perfect amount of water coupled with food then theoretically there should be no excretion.

Thank you water.

Sir could you upload parts 3 and 4 of the series.

FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CG2R53 NG2R51 CG2R53 (ATOMS 7400 7401 7425) ...hello....What can I do to solve this problem? thank you

Can single boiling bubble be simulated through gromacs

Thank you for the tutorial. In the most recent version, the grid box is non-transparent. Do you know how to regulate the tranceparency of grid box?

could you please post the rest of the videos?

Sounds a bit like pharmacy to me

Great webinar Girinath ji. I am new to this field basically motivated by understanding the bio-sensor design field. What simulation solution would work for studying the MD of proteins in vivo and their interaction with electromagnetic fields in various spectra from RF to NIR/IR and Visible light.

How to determine CMC (Critical Micelle concentration) of surfactants using COSMOtherm pls make a video relevent to that

Aging is much dependent on mitochondrial dysfunction.

Drug delivery process

How can I shorten it to just a few hours? That’s a much better option for me.

Wow ,i really love this aspect of chemistry ,i would love to the besf in this field .❤❤

sir please make tutorial of protein ligand simulation using own pdb thanks

Sir is this on window or Linux????

Sir plz make a tutorial video on virtual screening or docking by deep learning open access tools

Thank you so much. Please provide me with two articles and their DOIs so that I can cite them in one of my prepared articles. I plan to use QSARNIS after having truly benefited from your video as recognition.

Dear Professor, I am looking for postdoc position in your group

Amazing one sir !

We need a tutorial explain covalent docking with one Free software please Sir

Hello sir, I have a query. Do we need to add charges and hydrogen before protein-protein docking as well or is it only for protein ligand docking? Also, how can we find the active sites of predicted 3d structure? looking forward for a reply

Plz share the link to download this version

Dear Sir, Can you please provide me the Script file. Thank You ABJ

can you provide merge script for protein and ligand?

Hi sir, I am facing an error while installing Gromacs-2021 in google colab. The error is /usr/include/c++/11/type_traits:3071:7: note: ‘std::__is_complete_or_unbounded<std::__type_identity<gmx::IndexGroupsAndNames> >((std::__type_identity<gmx::IndexGroupsAndNames>{}, std::__type_identity<gmx::IndexGroupsAndNames>()))’ evaluates to false make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/build.make:21782: src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:4537: src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 make: *** [Makefile:166: all] Error 2 bash: line 9: /usr/local/gromacs/bin/GMXRC: No such file or directory --------------------------------------------------------------------------- CalledProcessError Traceback (most recent call last) <ipython-input-14-4536d1739ee2> in <cell line: 1>() ----> 1 get_ipython().run_cell_magic('bash', '', 'wget ftp://ftp.gromacs.org/gromacs/gromacs-2021.tar.gz tar xfz gromacs-2021.tar.gz cd /content/gromacs-2021 mkdir /content/gromacs-2021/build cd /content/gromacs-2021/build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA make -j 2 make install source /usr/local/gromacs/bin/GMXRC ') 4 frames <decorator-gen-103> in shebang(self, line, cell) /usr/local/lib/python3.10/dist-packages/IPython/core/magics/script.py in shebang(self, line, cell) 243 sys.stderr.flush() 244 if args.raise_error and p.returncode!=0: --> 245 raise CalledProcessError(p.returncode, cell, output=out, stderr=err) 246 247 def _run_script(self, p, cell, to_close): CalledProcessError: Command 'b'wget ftp://ftp.gromacs.org/gromacs/gromacs-2021.tar.gz tar xfz gromacs-2021.tar.gz cd /content/gromacs-2021 mkdir /content/gromacs-2021/build cd /content/gromacs-2021/build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA make -j 2 make install source /usr/local/gromacs/bin/GMXRC '' returned non-zero exit status 1.

HI sir, If I runnig a complex simulation, Can I go to my other work with the system at the same time?

Is there any video for docking of metal ligand and protein? If there is, please share with me

Sir…you clarified lot of doubts ….thank you so much for sharing your knowledge in a true way..and also appreciate the time you have invested in making such videos…👏👏👏

Sir can we link gromacs with python

How to perform hydrogen bonding analysis using molecular Dynamics

Dear Sir, Could you provide a tutorial on how to install, run, and analyze gmx_mmpbsa in jupyter notebook? It will help a lot. Thank you.

and the videos part 4/5 , 5/5 ??

Please, share too-solutions about fatal error to find bond parameters

Hi, I subscribed for Pay As You Go, but the out put results of MD simulation destroyed!!! Do you have any idea?

Hi professor. Thanks for their tutorial, they are very educational. I have a question, If I want to run MD simulations in a HPC cluster, In addition to the configuration file, should I also upload the parameter files (toppar folder)?

dear sir, i suspect bfee tutorial is not available?

Dear Sir, I have tried to use VMD with protein ID: 7E3H, however, I cannot generate psf file. Could you please help me with this issue? vmd-l: psfgen error: MOLECULE DESTROYED BY FATAL ERROR

I need to proceed 100 ns MD simulation, is it possible with Colab??

Excellent presentation, great teacher!

Thank you sir

Is it same way that gromacs work in google colab also?

How to obtain the potential for the protein alone.

Has blind docking ever brought us a medicine?blind docking with lowest binding energy i.e -10 can it be considered as a good inhibitor ?

Great piece of information on KNIME... highly helpful for beginners