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Need videos on free energy calculations gmx-mmpbsa

Need videos on free energy calculations gmx-mmpbsa

Need videos on free energy calculations gmx-mmpbsa

Need videos on free energy calculations mm-mmpbsa

Hello, Thanks for this tutorial. I followed the steps until I try to compile gromacs-2024.2. The program reported error during cmake. It reads like this: 'CMake Error at /usr/share/cmake-3.28/Modules/CMakeDetermineCUDACompiler .cmake:270 (message): Failed to detect a default CUDA architecture.' could you please tell me how to fix it?

Hello there, can you please tell me your system (PC/LAPTOP) specifications Thank you

sir can you pls help with this log in process they are saying you need to purchase an item

Good work ❤️ Thank you so much 😊

I got an error sir my cordinate file (box_sol.gro 23286) and topology file number( 21270 ) Did not match. Kindly help me . I follow your vedio since episode 8 till now it work smoothly but now this error arises

Very useful sir, thanks.

2619 atoms are not part of any of the T-coupling groups I am getting same error every time plzzz suggest what to do

Best <3

Sir forward primer always binds with anti sense strand and reverse primer binds with sense strand.

Please sir, can you please do this mac os!

Thank you for the tutorial! Very well explained and worked properly.

Thanks for your very informative video but I am getting Cmake error configuration file unable to detect cuda compiler Although I have installed cuda toolkit

Can I run gromacs md simulations in windows

You are a lifesaver. Everything works perfectly. Thank you so much for such a detailed presentation

sir am always trying to create ligand topologies from swissparam but there is always an error although i follow all the steps

Your explanation is mind-blowing 🎉 Plz make a vedio on SMART and TBtool

from the tutorial, i am failing to understand how the protein-ligand interaction in Pose1 is maintained. Does it differ, lets say i have used pose3 or i have downloaded the ligand in sdf format and just converted it to mol2 format using open babel. May you please help me.

Hi Why is there no alignment?

Hi Dear Vina linux pl is installed with vina or it is different ?

My Grace program does not open when entered xmgrace command

Thank you so much for this explanation, I will be using this software soon!

Thank you so much!

Thank you so much for the super awesome tutorial. A quick question, do we have to run the equilibration run for NVT and NPT for exactl same time as that of md run (for eg 25 ns for all, NVT, NPT and md run)? Please let me know, thanks a lot again for all the hard work.

How did you get the sequence of the reference strains?

Thank you so much even very know persons can't teach me this past 2 months lot of errors and mistakes finally I saw your video truly I can't got any errors successfully I done this thank you very much sir

Thank you so much sir. This video has been fundamental for me to learn MD simulation. Please upload video to calculate cross correlation matrix also. It is imperative for may work

downloading requires purchase. how to go about it

Thank you for your wonderful explanation, it helped me tremendously😁

Sir, can you explain how to run hole2 programme for protein pore calculation

Thanku sir for great tutorial..can you please share this package via drive link??

Hi Dr. Thank you for the wonderful lecture When converting to a topology file, I am getting an error that Residue 'BRL' is not found in residue topology databases. How can I solve this issue sir?

Thanks a lot...I could find only this video very useful...❤

Hi, I have run an MD simulations for 100ns on protein-protein complex, and I am currently trying to analyse the results. However, while I was running the simulations, there was a power cut-off on my PC and in order to continue the simulations, I extended the running time for another 20ns. unfortunately, when I tried to generate the RMSD plot, I noticed that the plot did not start from 0ns but from around 90ns, and the value of the RMSD just shoot to around 2.9-3.0nm. I also had another simulations run for 1ns, and the graph actually starts from 0ns point. So, I actually noticed that I have few parts of the xtc files and planned to combine them so I get to generate a continuous RMSD plot from 0ns to 120ns using this command gmx trjcat -f *.xtc -o fixed.xtc but I have been getting errors. Would you suggest any advice for me? Thank you in advanced.

Sir im finding this error CMake Error at cmake/gmxManageCuda.cmake:116 (enable_language): No CMAKE_CUDA_COMPILER could be found. Tell CMake where to find the compiler by setting either the environment variable "CUDACXX" or the CMake cache entry CMAKE_CUDA_COMPILER to the full path to the compiler, or to the compiler name if it is in the PATH. Call Stack (most recent call first): CMakeLists.txt:699 (include)

Sir, What is the reason that in Maestro, job is died automatically?

Please guide me, I am stuck as my consensus sequence is coming in this form. what to do? Example >Consensus -------------------------------------------CTGCCAGTAAGACAGGGATAACGCCCGGAAAC-GAAGCAAATAACGCATA--AACCACTCCGCCAGGGGAG-ACGATCGAAAGACGGAAACGCAAAGCAATT---GACGGGCCCCCGCA-CAAGAGCTAGAGCATGAGGTA-AAGGCGAACCAACGCAAAGAACCATACCAGACCTG-GACA-TCATCGGACA-ACT----CT-AGACCAAAAAACAAGGCTCAACCC-GGAGGGTAAGCGGAAACTCGCCAGCCCGAAA-CACCCAGATAATCC-------------------

Thanks a lot!

Really helpful video thank you, sir...

It is taking a long time for nvt equlibration....what should I do!?...while running the cursor us also stop blinking! Please it's urgent kindly let me know

In my mega the scale is not showing can you help in this

I only have sequence for single primer can I submit the sequence?

what if we want to change the ph of solvent?

Very Very informative and easy to understand. Thank you so much Dr

How about for 4peaks?

Very helpful tutorial. Can u make a video on protein-protein MD simulations or can guide which server or method will be best for macromolecule interactions?

very informative and easy to understand. Thank you Dr