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2 жыл бұрын
2 жыл бұрын
2 жыл бұрын
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@metariarsitalia6568 15 күн бұрын
hallo, i had following ur tutors and can’t find the build on that file after downloading. so whats should i do?😢
@al1r3z49 15 күн бұрын
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.
@metariarsitalia6568 15 күн бұрын
@@al1r3z49but sorry, how can i use cmake? if cmake isn’t recognized? 😢
@skobichevskii 15 күн бұрын
how can i find out the binding energy?
@al1r3z49 15 күн бұрын
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.
@abdurrahmanusman6701 Ай бұрын
Hi there! Thanks for the tutorial. I am having a problem building Gromacs. At first, it couldn't locate OpenCL, but I wrote a script that directed it to where OpenCL is on my PC, and that solved it. However, I encountered a new challenge with an error message requiring OpenCL version 1.2 or newer. My PC has version 3 installed, but it didn't work. I also set and used version 1.2, but I still received the same response. I restarted my PC, but the problem persists. I am looking for more guidance. Thank you.
@anandarup-bnk Ай бұрын
First of all, thanks a lot for the wonderful tutorial. Just wondering if you could help me with the compilation of GROMACS 2024.2 on Windows with NVIDIA CUDA support. Can you?
@PremanandA-e4s Ай бұрын
Why to Choose 3 C-alpha (for least square fit) and 13 LIG (for covariance analysis) ? Shouldn't we choose same group for PCA ? If protein ligand complex is to be selected, shouldn't we chose 22 (Protein_LIG) ?
@Goldentear2011 2 ай бұрын
Your tutorial is very useful for me. Thank you very much. ❤
@saalsjdh 2 ай бұрын
Hello, I have the following problem: C:\Gromacs\gromacs-2024.2\build>cmake --build . --config Release --parallel MSBuild version 17.10.4+10fbfbf2e for .NET Framework MSBUILD : error MSB1009: Project file does not exist. Switch: ALL_BUILD.vcxproj I followed all your steps up to this point with no typose. What should I do?
@kshitijmohan6987 3 ай бұрын
Very helpful video!! Can you create a tutorial for quandlelabs using this?
@farshadhamekhani4707 3 ай бұрын
Can i have ur email ?!
@al1r3z49 3 ай бұрын
Sure, it's [email protected]
@arshasnair2772 3 ай бұрын
how to calculate interaction energy using desmond maestro
@al1r3z49 3 ай бұрын
I haven't work with Schrodinger maestro. But I will look into it.
@nandhiniphysics299 4 ай бұрын
How to conform 89% variance are cummulated using eginval.xvg file
@VR-pg4uv 4 ай бұрын
fROM WHERE THE XYZ AND RADIUS DATA CAN OBTAINED
@al1r3z49 4 ай бұрын
You can use CavityPlus web server
@MinaYari-vr2bn 4 ай бұрын
Your video is really useful, thanks 🙏🙏
@al1r3z49 4 ай бұрын
Thanks for watching
@Tur_Martinelli 5 ай бұрын
thanks man! helped a lot!
@durdonamalikova4915 5 ай бұрын
I saw your video from Uzbekistan.
@al1r3z49 5 ай бұрын
Great. Thank you dear Durdona ♥️
@durdonamalikova4915 5 ай бұрын
Thanks a lot ❤
@nagashreesankarshan2092 5 ай бұрын
Hi, while executing the command at 2:42 I was getting the following error... CMake Error at CMakeLists.txt:7 (project): Generator Visual Studio 17 2022 could not find any instance of Visual Studio. -- Configuring incomplete, errors occurred! Please help in rectifying this error.
@al1r3z49 5 ай бұрын
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.
@baronwichern7082 5 ай бұрын
*Promosm* 🎶
@arunannamalai0364 5 ай бұрын
I am getting a LINK error for this: C:\GROMACS\gromacs-2024.1\build>cmake --build . --config Release --parallel LINK : fatal error LNK1181: cannot open input file 'VkFFT.lib' [C:\GROMACS\gromacs-2024.1\build\src\programs\gmx.vcxproj] What shd I do?
@al1r3z49 5 ай бұрын
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.
@arunannamalai0364 5 ай бұрын
Thanks for responding... I got it installed after retrying and following your procedure...
@al1r3z49 5 ай бұрын
@arunannamalai0364 That is great news, and I am very happy to hear that.
@ionamassey9923 5 ай бұрын
Thank you so much for this wonderful video. Although i have one doubt which group needs to be selected for pca Analysis of protein ligand complex and for protein alone
@al1r3z49 5 ай бұрын
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.
@ionamassey9923 5 ай бұрын
@@al1r3z49 Okay
@ES-yd1ze 6 ай бұрын
Depend on what you are choseing Time 34 in first command??
@al1r3z49 6 ай бұрын
There are several way to find out when is your system convergence time. I have used RMSD. at 34ns the fluctuation was minor.
@ES-yd1ze 6 ай бұрын
@@al1r3z49 excuse me sir rmsd or rmsf
@al1r3z49 6 ай бұрын
@@ES-yd1zeBoth can be used. For example, RMSD or RMSF should reach a plateau indicating stable protein structure, it also can be visually assessed.
@ES-yd1ze 6 ай бұрын
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 6 ай бұрын
Hi Doctor how can I contact with you sir Please
@al1r3z49 6 ай бұрын
Hello dear sir. You can always have contact with me by this email: [email protected] Sorry for late replay. Best Alireza
@hanstsahnang4533 6 ай бұрын
Hello thanks for the video. How can pca analysis be performed using desmond
@al1r3z49 6 ай бұрын
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
@hanstsahnang4533 6 ай бұрын
Hello thanks for the video. How can pca analysis be performed using desmond
@al1r3z49 6 ай бұрын
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
@VenuBattena 6 ай бұрын
Dear sir how to identify the variation percentage between PC1, PC2 and PC3 and how to represent the data in scatter plots ?
@al1r3z49 6 ай бұрын
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
@VenuBattena 6 ай бұрын
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
@darkotaku16 7 ай бұрын
Could you show the piece of the video where you copy the .dll to the GMX bin folder?
@al1r3z49 7 ай бұрын
Dear friend, I think it was in /Gromacs/GMX/bin/
@darkotaku16 7 ай бұрын
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?
@al1r3z49 7 ай бұрын
@@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
@monzecobak 7 ай бұрын
Thank you so much for all your valuable videos!
@al1r3z49 7 ай бұрын
Thanks for watching.
@ducky36F 8 ай бұрын
Does biology degree .... Has to do this **** with zero IT training.
@al1r3z49 8 ай бұрын
I am not sure, but training bioinformatics requires some computation knowledge.
@edithmargaritaangulorodrig5260 8 ай бұрын
Excuse me, I have a little problem with windows, when i try installed my computer detect it like a virus, Why? Can you help me?
@al1r3z49 8 ай бұрын
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.
@edithmargaritaangulorodrig5260 8 ай бұрын
@@al1r3z49 Thank you very much.
@sajadyaghoubizadeh8416 9 ай бұрын
Hi Alireza, Good job and thanks a lot for tutoring, but is it possible for you to make interpretations for figures? I think it would be the best if you do that too. Anyway it is just a suggestion. Thanks again
@al1r3z49 9 ай бұрын
Thanks for watching. Sure I will.
@a.rakhayaseen5447 9 ай бұрын
3:01 facing this error: C:\GROMACS\fftw-3.3.10\build>cmake --install . --config release --prefix C:\GROMACS\fftw-install CMake Error at cmake_install.cmake:51 (file): file INSTALL cannot find "C:/GROMACS/fftw-3.3.10/build/Release/fftw3f.dll": File exists. in the fftw_install folder only bin and lib files are there no include folder generated any solutions??
@al1r3z49 9 ай бұрын
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.
@a.rakhayaseen5447 9 ай бұрын
@@al1r3z49 its ok i have figured it out using ubuntu
@uneven3166 9 ай бұрын
how to sort the ligands with least binding energy to high?
@al1r3z49 9 ай бұрын
The affinity is listed according to high to low. However, you can manually sort them in MS-Excel.
@uneven3166 9 ай бұрын
can we use gromaxs on UseGalaxy server? If yes, then how much time it will take for 100ns run?
@al1r3z49 9 ай бұрын
Yes you can. There is also a good tutorial on that in UseGalaxy server.
@docentejairoenriquemercado5530 10 ай бұрын
Is it necessary to download gmx-MMPBSA?
@Endrin85 10 ай бұрын
Hello! How to define the number of principal components (PC) in a PCA?
@al1r3z49 10 ай бұрын
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.
@mohsen_ej 10 ай бұрын
Hi Alireza. I hope everything goes well for you. I appreciate your tutorial on installing Gromacs. However, I faced a problem in Gromacs installation step. after I run: "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", The error is: "-- Selecting Windows SDK version 10.0.22621.0 to target Windows 10.0.22631. -- Checking for module 'mpi-c' -- Can't find mpi-c.pc in any of C:/Strawberry/c/lib/pkgconfig use the PKG_CONFIG_PATH environment variable, or specify extra search paths via 'search_paths' -- Checking for module 'mpi-cxx' -- Can't find mpi-cxx.pc in any of C:/Strawberry/c/lib/pkgconfig use the PKG_CONFIG_PATH environment variable, or specify extra search paths via 'search_paths' -- GPU support with OpenCL is deprecated. It is still fully supported (and recommended for AMD, Intel, and Apple GPUs). It may be replaced by different approaches in future releases of GROMACS. -- Found OpenCL: C:/Program Files (x86)/IntelSWTools/system_studio_2020/OpenCL/sdk/lib/x64 CMake Error at cmake/gmxManageOpenCL.cmake:51 (message): OpenCL is not supported. OpenCL version 1.2 or newer is required. Call Stack (most recent call first): CMakeLists.txt:665 (include) -- Configuring incomplete, errors occurred!" I'm so sorry for my long comment, but, it would me highly appreciated if you could have a look at this matter and let me know if you know how to deal with this problem. Many thanks. Mohsen
@al1r3z49 10 ай бұрын
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.
@fatemehsanaaskari3177 10 ай бұрын
👍
@БөхцоожЛхагвадорж 10 ай бұрын
how to open build tool on visual studio sir. I just downloaded it and it showed community tool command and I couldnt change it to build help me please
@al1r3z49 10 ай бұрын
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.
@БөхцоожЛхагвадорж 10 ай бұрын
@@al1r3z49 thanks sir
@agarwalsachin814 11 ай бұрын
Hello sir, I am facing errors while installing gromacs 2022 with cuda 12 ... please help me to resolve this issue
@al1r3z49 11 ай бұрын
Hello sir, there might be few options to solve this issue. Try: cmake -DGMX_GPU=CUDA .. Then: make make install
@anindogamingbd2512 11 ай бұрын
Hlew sir, Can you please give me a example file of your .ndx file. or help me to create one. Thanks in advance
@al1r3z49 11 ай бұрын
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.
@pravalsingh-o1e 11 ай бұрын
Respected Sir, How you have selected convergence time 34 ? and what you have putted in index.ndx file ?
@al1r3z49 11 ай бұрын
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.
@pravalsingh-o1e 11 ай бұрын
@@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
@VenuBattena 11 ай бұрын
sir, how to get free energy surfaces after md simulation between protein and drug...can you tell the coomand line of the gromacs ?
@al1r3z49 11 ай бұрын
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.
@venukrishna3683 11 ай бұрын
@@al1r3z49thank you so much for your response sir....
@Anu-mp9en Жыл бұрын
Sir, Can we use the pdbqt files for pyrx software also?
@al1r3z49 11 ай бұрын
Sorry for my late answer. Yes you can, I think it has also tools for analyzing docking interactions too.
@rizkiamaliaputri3740 Жыл бұрын
Thank you for the information, but I still have some questions about PCA analysis. I performed the peptide-membrane MD Simulations, I want to analyze the PCA only for the peptide, Is it possible to do it? and If it is possible, can you tell me how to do it? Thank you.
@al1r3z49 Жыл бұрын
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.
@rizkiamaliaputri3740 11 ай бұрын
@@al1r3z49 Thank you so much.
@rizkiamaliaputri3740 11 ай бұрын
It was very helpful.
@shirasagi9390 Жыл бұрын
sir, i really appreciate your video and find it easy to follow, however when i try to do the step from 5:56, i get these errors (cut short because the message would be too long otherwise) : C:\Gromacs\gromacs-2023.2\build>cmake .. -G "Visual Studio 17 2022" -A x64 -DCMAKE_INSTALL_PREFIX=C:\Gromacs\GMX -DGMX_BUILD_OWN_FFTW=OFF -DFFTWF_INCLUDE_DIR="C:\Gromacs\fftw-install\include" -DFFTWF_LIBRARY="C:\Gromacs\fftw-install\lib\fftw3f.lib" -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=OpenCL -DGMX_FFT_LIBRARY=fftw3 -- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway. If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on. -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- GPU support with OpenCL is deprecated. It is still fully supported (and recommended for AMD, Intel, and Apple GPUs). It may be replaced by different approaches in future releases of GROMACS. -- Looking for CL_VERSION_3_0 -- Looking for CL_VERSION_3_0 - not found -- Looking for CL_VERSION_2_2 -- Looking for CL_VERSION_2_2 - not found -- Looking for CL_VERSION_2_1 -- Looking for CL_VERSION_2_1 - not found -- Looking for CL_VERSION_2_0 -- Looking for CL_VERSION_2_0 - not found -- Looking for CL_VERSION_1_2 -- Looking for CL_VERSION_1_2 - not found -- Looking for CL_VERSION_1_1 -- Looking for CL_VERSION_1_1 - not found -- Looking for CL_VERSION_1_0 -- Looking for CL_VERSION_1_0 - not found -- Could NOT find OpenCL (missing: OpenCL_LIBRARY OpenCL_INCLUDE_DIR) CMake Error at cmake/gmxManageOpenCL.cmake:55 (message): OpenCL not found. Call Stack (most recent call first): CMakeLists.txt:661 (include) -- Configuring incomplete, errors occurred! what should i do ? is the error because i don't have openCL ? i am not a programmer and don't understand anything
@nilsazli4627 Жыл бұрын
When I execute the code at 2:24, it says "'cmake' is not recognized as an internal or external command, operable program or batch file." I get an error. What should I do for this?
@al1r3z49 Жыл бұрын
Please open your visual studio's command prompt, and type : pip install cmake. By this you will have cmake on you system.
@alichem8 Жыл бұрын
Hi Alireza, I followed your instructions but was not able to install it. On the 5:56 I got error ;
@al1r3z49 Жыл бұрын
Dear Alireza, could you please describe me your problem exactly, and write me your error? regards
@alichem8 Жыл бұрын
@@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
@al1r3z49 Жыл бұрын
@@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.
@bubat030 Жыл бұрын
do the newer zinc databases have pharmacopore search options aswell?
@al1r3z49 Жыл бұрын
I am not sure my friend.
@yagyeshkapoor908 Жыл бұрын
How to calculate MMPBSA binding energy from this??
@al1r3z49 11 ай бұрын
Sorry for my late replay. I am currently working on it to make a video.
@cake975 Жыл бұрын
if babel.exe doesnot work then copy paste obabel.exe in the ligand file and write obabel in the command line. Mine worked that way!! Thank YOU!
@al1r3z49 Жыл бұрын
It's great to hear that my friend.
@cake975 Жыл бұрын
@@al1r3z49 Thank you for such a savior video! After these steps, are these ligands ready to dock or do we need to do further steps for ligand preparation for docking?
@al1r3z49 Жыл бұрын
@@cake975I would check some ligands to make sure they are in their right conformations, having hydrogen and be in 3D format.