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Thank you for watching.

Hello. I am very glad that you watched the video. Please check the build folder after executing the command. If the files are not generated, I recommend starting over and directing the command line to the build folder, then starting to execute the command.

@@al1r3z49but sorry, how can i use cmake? if cmake isn’t recognized? 😢

Dear sir, the binding energy is an output of the docking results. For example, you can see the binding free energy after docking with Autodock. In this video, I have only show how to present or visualize the docking, meaning how the ligand is attached or posed in its biding site within the receptor.

Sure, it's Alirezaa2s@gmail.com

I haven't work with Schrodinger maestro. But I will look into it.

You can use CavityPlus web server

Thanks for watching

Great. Thank you dear Durdona ♥️

I am really sorry for my late answer. The installation process is quiet tricky, and it took me ~6 month to make it work, as I am not an expert, and I had experienced lots of errors, and this video is the final edition. I hope the following helps you out my friend: make sure that that Visual Studio 17 2022 is installed on your system. Reset Cmake, and set the visual studio path like this for example: > set "Visual Studio=C:\Program Files\Microsoft Visual Studio\2022\Community" Run cmake, and check cmake generator: > cmake -G "Visual Studio 17 2022" .. I eager to see your feedback sir.

I am really sorry for my late answer. The installation process is quiet tricky. This error indicates that the linker is unable to find the input file VkFFT.lib. Please make sure that you have all the necessary dependencies installed and properly configured.Also check Typos error during writing commands.

Thanks for responding... I got it installed after retrying and following your procedure...

@arunannamalai0364 That is great news, and I am very happy to hear that.

Thank you for watching. I will upload a new video in the next couple of days and explain how to calculate the cumulative variance in each PC, and how to select components with higher variances.

@@al1r3z49 Okay

There are several way to find out when is your system convergence time. I have used RMSD. at 34ns the fluctuation was minor.

@@al1r3z49 excuse me sir rmsd or rmsf

@@ES-yd1zeBoth can be used. For example, RMSD or RMSF should reach a plateau indicating stable protein structure, it also can be visually assessed.

Thank you very much sir for answer also I want to ask about -last value You are using 3 can I change the value like 4 and this depends on what sir ​? @@al1r3z49

@@ES-yd1ze I have the same question sir @al1r3z49

Hello dear sir. You can always have contact with me by this email: alirezaa2s@gmail.com Sorry for late replay. Best Alireza

Dear Sir, Hello. I am sorry for late reply. I haven't work with desmond for MDS. But as a rule of thumb, before starting PCA, make sure you have both a MD trajectory file (.dtr) and its matching topology file (.cms) ready. In the Simulation Preparation interface, you should upload your system's .cms and .dtr files and choose the molecule you are interested in. Afterwards, determine the covariance matrix of atomic positions by initiating PCA via Tools > Simulation Tools > Principal Component Analysis, then adjust settings like trajectory selection, atom choice, frame range, and output location. Perform the computation, enabling Desmond to produce eigenvectors and eigenvalues representing main motion modes. Examine the findings within Desmond or export them for external visualization, projecting the trajectory onto principal components to observe system motion. Keep in mind that details may differ depending on the version of Desmond, so refer to the manual for accurate guidance. Regards Alireza

Dear Sir, Hello. I am sorry for late reply. I haven't work with desmond for MDS. But as a rule of thumb, before starting PCA, make sure you have both a MD trajectory file (.dtr) and its matching topology file (.cms) ready. In the Simulation Preparation interface, you should upload your system's .cms and .dtr files and choose the molecule you are interested in. Afterwards, determine the covariance matrix of atomic positions by initiating PCA via Tools > Simulation Tools > Principal Component Analysis, then adjust settings like trajectory selection, atom choice, frame range, and output location. Perform the computation, enabling Desmond to produce eigenvectors and eigenvalues representing main motion modes. Examine the findings within Desmond or export them for external visualization, projecting the trajectory onto principal components to observe system motion. Keep in mind that details may differ depending on the version of Desmond, so refer to the manual for accurate guidance. Regards Alireza

My dear friend, sorry for late replay. IF you want to see the values for each PCs when you run a PCA analysis, you will receive a list of eigenvalues, typically ordered by magnitude. These eigenvalues indicate the variability across each principal component. You can simply drag and drop .xvg file into the grace software to see the eigenvalues through the PCs. After that, to identify the variation percentages, you can divide the eigenvalues of each PC by the total variance (sum of for example first five PCs) and multiply by 100. For demonstrating the variations covered by the selected PCs, scree plot is more common. But, you can draw a scatter plot for example every frame in your trajectory is linked to PC scores indicating the level of contribution of each frame to each PC. For a scatter plot, choose three PCs to five first PCs, and display the PC scores of your frames on the selected PCs. Every point on the graph corresponds to a frame and indicates its location within the PC space. I hope this replay helps you Regards Alireza

Thankyou so much for your information friend. In research article for the PCA analysis , the people are using Bio3D galaxy Australia server for analysis and visualization of PCA . Do you know it is worked or not tight know? Am getting errors if run the analysis.@@al1r3z49

Dear friend, I think it was in /Gromacs/GMX/bin/

Dear @al1r3z49, at time 9:46 you mention adding some .dll files to the /Gromacs/GMX/bin/ directory, but you don't mention where you get the .dlls from For my part, I tried to get fftw3f.dll from the fftw-install/bin directory and fftw3f.lib from the fftw-install/lib directory, but the other file fftw3.dll where do you get it from?

@@darkotaku16Sorry for misunderstanding. The .dll files are within the .zip file of fftw3, which can be accessible from the following link: www.fftw.org/install/windows.html Note: I think I showed the download link in the video. Bests Alireza

Thanks for watching.

I am not sure, but training bioinformatics requires some computation knowledge.

The virus detection is because of Crack.exe file. Do as follow: Go to Start > Settings > Update & Security > Windows Security > Virus & threat protection. Under Virus & threat protection settings, select Manage settings, and then under Exclusions, select Add or remove exclusions. Select Add an exclusion, and then select from files, folders, file types, or process.

@@al1r3z49 Thank you very much.

Thanks for watching. Sure I will.

The fftw3f.dll file cannot be find. I have a part in the video, where I copy the .dll files in a directory. At the end of installation. Unfortunately, this process may vary. I will look into it, and replay.

@@al1r3z49 its ok i have figured it out using ubuntu

The affinity is listed according to high to low. However, you can manually sort them in MS-Excel.

Yes you can. There is also a good tutorial on that in UseGalaxy server.

Hi, I look in eigenvalues.xvg by notepad. Usually first eigenvectors, for example first five vectors, contains much of the values. It is your option to select how much of the vectors. Usually, first 3 or 5 vectors are ok.

Dear Mohsen, Hi, The error you're encountering indicates that CMake is not able to find the required OpenCL headers or libraries. It appears that you have OpenCL installed, but the version is not compatible with GROMACS. If I am not mistaken, I used OpenCL v2.0. In the following I show you the alternative options, and if the error you get persist, put -DGMX_GPU=OFF. GROMACS requires OpenCL version 1.2 or newer. The path you provided suggests that you have the Intel OpenCL SDK installed. Make sure that the OpenCL-related environment variables are set correctly. In particular, the OpenCL_INCLUDE_DIR and OpenCL_LIBRARY variables need to be set to the correct paths. You can set them in the CMake command as follows: cmake .. -G "Visual Studio 17 2022" -A x64 -DCMAKE_INSTALL_PREFIX=H:\Gromacs\GMX -DGMX_BUILD_OWN_FFTW=OFF -DFFTWF_INCLUDE_DIR=H:\Gromacs\fftw-install\include -DFFTWF_LIBRARY=H:\Gromacs\fftw-install\lib\fftw3f.lib -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=OpenCL -DGMX_FFT_LIBRARY=fftw3 -DOpenCL_INCLUDE_DIR=C:/Program Files (x86)/IntelSWTools/system_studio_2020/OpenCL/sdk/include -DOpenCL_LIBRARY=C:/Program Files (x86)/IntelSWTools/system_studio_2020/OpenCL/sdk/lib/x64/OpenCL.lib Unfortunately, I have removed my raw videos of this video, since I got too many errors during 6 month of my attempt to compile GROMACS on Windows, and I might had a similar error on my way. However, if you find that you have an older version of OpenCL, consider updating it to a version that meets the requirements. Try these steps, and if you still face issues, please provide additional information about your OpenCL installation and GROMACS version.

My dear friend sorry for the late reply. If you mean to make and enter the build directory within the Gromacs folder, you can open up the Visual studio and launch the developer command prompt from the Visual studio Build tool. The just copy the GROMACS directory root. Then do as follow: cd "gromacs_root (past here)" mkdir build cd build Again, thank you for watching this video.

@@al1r3z49 thanks sir

Hello sir, there might be few options to solve this issue. Try: cmake -DGMX_GPU=CUDA .. Then: make make install

Here is an example of .ndx file: [ System ] ; Entire system 1 2 3 4 5 6 7 8 9 10 [ Protein ] ; All protein atoms 1 2 3 4 5 6 7 8 9 10 [ Protein Backbone ] ; Protein backbone atoms (CA, N, C, O) 1 2 3 4 [ Ligand ] ; Atoms belonging to a ligand 5 6 7 [ Water ] ; Water molecules 8 9 10 You can generate by: gmx make_ndx -f your_topology.tpr After selecting your desired group type q and hit enter.

The convergence time of 34 (or any specific value) in the context of molecular dynamics simulations is not a standard or fixed value. The choice of convergence time is typically a user-defined parameter and depends on the specific goals of your simulation and the properties you are studying. As for the index.ndx file, this file defines groups of atoms that you want to analyze or manipulate in your GROMACS simulations. For me it was a ligand atoms which can be generated by gmx make_ndx.

@@al1r3z49 Respected Sir, Few files are generated with all this can you please describe about it what they represent and how to describe each figure in manuscript. I am doing protein-ligand simulation. These set of files are generated: average.pdb, eiginval.xvg, eigcomp.xvg, eigrmsf.xvg, 2dproj.xvg. It would be a great help if you can provide few inputs regarding this. Thanking you kind regards

Dear Sir, I am sorry for delayed response. You may consider potential of mean force (PMF) by umbrella sampling or energy module for calculating interaction energies. In the following I write some examples to perform umbrella sampling and PFM analysis. However, please see the GROMACS documentations; # Create index file (index.ndx) to define the drug molecule gmx make_ndx -f system.tpr -o index.ndx # Generate position restraint file (position_restraints.itp) gmx genrestr -f system.tpr -n index.ndx -o posre.itp -fc k -dist 0.1 # Perform pulling simulation gmx mdrun -s pulling.tpr -deffnm pulling -cpi pulling.cpt # Analyze umbrella sampling data and compute the PMF gmx wham -it tpr-files.dat -if pullf-files.dat -o profile.xvg -hist histo.xvg -unit kJ Do not hesitate to give me a feed back, and help me to improve my understanding of the process.

​@@al1r3z49thank you so much for your response sir....

Sorry for my late answer. Yes you can, I think it has also tools for analyzing docking interactions too.

You firstly need to make an index for you desired atoms by typing: gmx make_ndx -f your_trajectory.xtc -s your_topology.top select the options represent your peptide atoms. Then use the following and extract your peptide atoms' trajectories: gmx trjconv -f your_trajectory.xtc -s your_topology.top -n your_index.ndx -o peptide_trajectory.xtc Then continue to analyze PCA by gmx covar and gmx anaeig.

@@al1r3z49 Thank you so much.

It was very helpful.

Please open your visual studio's command prompt, and type : pip install cmake. By this you will have cmake on you system.

Dear Alireza, could you please describe me your problem exactly, and write me your error? regards

@@al1r3z49 Yes I sent you by email. Overally I would like to know your idea of is it better to install it directly on windows or first install a Linux platform and then install the Gromacs. I am a little bit confused. Thanks

@@alichem8 I am currently working on your issue. However, working on a virtual machine or ubuntu linux is much easier. If you are not willing to change your OS, and using MS-Windows 10/11 you can open Microsoft Store and search/install Ubuntu version 16 or 18. By searching ubuntu from the start menu you will have access to a lockal linux service which is a good choice for working easily with Gromacs.

I am not sure my friend.

Sorry for my late replay. I am currently working on it to make a video.