MMPBSA analysis of protein ligand using gmx_mmpbsa for gromacs trajectories
ฝัง
- เผยแพร่เมื่อ 11 ก.ย. 2024
- For research purposes
Gromacs trajectories can be used.
Contact me on-
Email:- vijayitsbbd@gmail.com
You can use following commands-
1. Environment creation
sudo apt install openmpi-bin libopenmpi-dev openssh-client
sudo apt-get install python
sudo apt-get install python3-pip
sudo apt-get upgrade
sudo apt-get update
2. Installation of miniconda
curl -O repo.anaconda....
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh
3. Installing gmx_mmpbsa
conda update conda
conda create -n gmxMMPBSA python=3.9 -y -q
conda activate gmxMMPBSA
conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers -y -q
python -m pip install git+github.com/Val...
python -m pip install pyqt5
python -m pip install gmx_MMPBSA
4. Testing the gmx_mmpbsa
gmx_MMPBSA_test
5. Running the gmx_mmpbsa
gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci index.ndx -cg 1 13 -ct md_0_1_noPBC.xtc -cp topol.top
Really Enjoyed your lecture Sir. I think this is one of the most comprehensive description of gmx_mmpbsa.
Thank you❤
Professor, I would to thank you so much! I was really need of these analysis in my work!
Thank you so much Sir for the detailed explanation
installation tutorial is very well explained; thanks
Thanks a million times i could finally install it
Thank you Sir for this insightful video.
Thank you sir. You are amazing!
Dear Sir,
I am a beginner for computational chemistry. I want to do Protein protein interaction and protein ligand interaction. I have installed gromacs and followed all your TH-cam videos. Thank you alot. I learnt so many things from it.
But sir, during analysis of those result I face problem.
Would you mind sharing some materials such as research article or reliable source which I can follow to understand the analysis of protein ligand interaction such as rmsd, rmsf, rg, SASA, PCA or MMPbsa in detail.
Kindly consider my request, I'll be always grateful to you.
Thank you.
Sincerely yours,
Deenbandhu Sharma
Thank you so much professor
dear sir,
I am completed MD Simulation for protein_ligand complex. After proceed for MMPBSA analysis using gmx_MMPBSA method and In this results delta total energy is 551.03 . Can you explain why delta total energy is positive and high? How to solve this issue?
Thank you Sir. Can you please make video of how to analyze the PCA analysis and salt bridges analysis.
I will try
Dear Sir,
I am a beginner for computational chemistry. I want to do Protein protein interaction and protein ligand interaction. I have installed gromacs and followed all your TH-cam videos. Thank you alot. I learnt so many things from it.
But sir, during analysis of those result I face problem.
Would you mind sharing some materials such as research article or reliable source which I can follow to understand the analysis of protein ligand interaction such as rmsd, rmsf, rg, SASA, PCA or MMPbsa in detail.
Kindly consider my request, I'll be always grateful to you.
Thank you.
Ok email me I will share with you
Thank you sir
Sir in the output file there is not entropy result. How to find the TΔS to calculate the final binding energy
Professor, I verified that the Valdes Tresanco link is not working. Do you have another option at this stage?
Show me links
thankyou sir
Welcome
sir I am getting the following error.
some energy terms are undefined,
I am using a protein that has got two chains, is the error arriving because of this ?
This is not a mistake please go through the gmx_ mmpbsa user forum.
To be more specific about the error: 'MMPBSA_Error: Could not find necessary program [ GROMACS ]' this error is seen in the log file.
First export gromacs using this command
source /usr/local/gromacs/bin/GMXRC
Or
export CMAKE_PREFIX_PATH=/usr/local/gromacs
After the last command it shows MMPBSA_Error:
You must define the structure, topology and index files, as well as the group
Dear, I think you have not using proper topology or index file.
While installing miniconda, on running the second command chmod..
It is showing cacnot access ' miniconda 3-latest-linix-x86-64.sh: no such file or directory.
How can I solve this issue. Please help me
Your download is not successful so first check the downloaded file.
Thank you for this tutorial. Everything was good until analysing part. How can I open the analyser GUI? Please help
Configure your wsl as version 2. It support gui.
Dear sir, thank you for your tutorials sir. Sir can pls make a tutorial to work with autogrow for fragment based drug design
Ok
You can also subscribe the channel
I have sir along with my frnds
@@sethupathiraj ok
Autogrow*
Thankyou professor for the great video, I got error while testing is that a big problem
Activate gromacs before testing
@@chemvigyan8518 yes sir I use command conda activate gmxMMPBSA
Hello sir I got error such as gmx_ _ MMPBSA doesn't support water/ions molecules in any structure but we found 35815 molecule in the complex.
Send me screen shot of error
Dear Sir,
Do we need to do any preprocessing of the XTC trajectory file before proceeding with gmx_MMPBSA calculations? Kindly suggest
Just correct the trajectory as in video of protein in water simulation.
@@chemvigyan8518 Sir are you referring to the protein Lysozyme in water video can you please share the link of the video
@@rahulnarayan12 th-cam.com/video/zxnJDiz3irs/w-d-xo.html
Dear sir, as suggested I tried installing both in root only. I got the installation right. However, during the test run I got errors. This error is different as shown below.
MMPBSA_error: /use/local/gromacs/bin/gmx make_ndx failed when querying index.ndx.
Except one test passed (comp_receptor) without error
Rest 8 failed.
Even I am facing the same error sir. I am not using ubuntu, I installed this in centos 7. Is there any changes that should be done in the command line? could you please help me out sir.
Import gromacs before running the test.
@@varshaachuthan7333 I think command will be same but however I suggest to post your query in gmx_mmpbsa mailing group.
Hello Sir.
I am a beginner in this field.
md_0_1_noPBC.xtc = md_0_1.xtc?
how do I get this md_0_1_noPBC.xtc file.
Please
Sir for.the installing it is taking time sir it's been for one hour it shows ... Solving environment working... 😭 What to do sir ... Please reply sir
Not sure may be internet issue. Wait to complete.
Hi my teacher, I said in your previous video that I had problems calculating energy after the md simulation. With this video, I successfully made the calculation with gmx_MMPBSA. Thank you very much. But is it normal for the binding energy to be zero? I also want to calculate energies such as solvent accessible surface area (SASA) and solvent accessible volume (SAV). Is there a command for this?
If binding energy is negative means minimum energy maximum stability of protein ligand complex. Go to playlist and sea video on g_mmpbsa, by this you can calculate SASA and SAV.
@@chemvigyan8518 Min energy=max stability-I know that, teacher. In the receptor-ligand relationship I simulated MD for 100 ns in GROMACS 2022, the binding energy results in an average of about 2700 kJ/mol, while I cannot understand g_MMPBSA results in 0 in the calculation. Does this mean that the two are not connected at all, sir?
@@945corleone I think binding is poor and bonds break during course of simulation so you getting average as zero. You can analyze hbond to confirm it.
@@chemvigyan8518 I've already done that, sir. The receptor-ligand pair formed a maximum of 8 hydrogen bonds and a maximum of 10 contacts.
@@945corleone what is minimum number, how much bonds persist during whole time period of simulation. What is ns of your simulation.
Hi sir, I've got an error while running the gmx_mmpbsa command stating
IndexError: list index out of range
can you please explain about it
No idea
You can directly ask to the author of program.
Or
Paste your query in gmx mailing group
Dear @Chemvigyan Please tell me can positive value of delta G be obtained if ligand (known inhibitor) binding affinity is high?like in this video you obtained 12.78 kcal/mol delta G value. Is it okay?
Not okey, binding energy must be negative. but here gmx consider the PB energy. So we have to left the PB energy, then it will be fine. However the main purpose is how to use the software to get the result.
@@chemvigyan8518 how to exclude the PB energy
@@chemistryforall-bynsridhara the previous statement made by me is quite wrong. Since calculation is for pbsa analysis, hence pb energies cannot be separated. But one want to add here that, binding energy must be negative but sometimes we get positive energy as in by case leads to destabilization of system. However, I hope you all get the negative value. Here my focus is only to show the steps, to perform the analysis and running the command.
Hello Sir,
I followed the above steps
MMPBSA_Error Could not find necessary program [ GROMACS ]
I am getting the above error. I understand that my GROMACS is installed in root and I have done the installation of gmx_MMPBSA in the local path. Can you please help me with the above? Can we do the entire installation again in root is this ok
First export gromacs
If it doesn't work the try to install in local path or root
Thank you very much sir. Will this be compatible with gromacs 2022.2?
Writing for your reply. Thank you.
Yes, to the latest version also
Thank you sir, I will try.
Hi sir.
I would like to carry out the MM-PBSA study, and I have the GROMACS - gmx version, 2022.4.
can I carry out this study with the steps you have explained.
Thankks
Yes
Use only charmm or amber force field
@@chemvigyan8518 ok
Sir after moving to the directory i was unable to creat the new folder within directory what should i do now?
Turn terminal as administrator
thank you, sir, sir, how to plot a graph please sir upload a video
I successfully installed gmx_mmpbsa following your video. But when tried to submit for gmx_mmpbsa calculation, it shows gmx_mmpbsa command not found. What should I do now. It would be favourable if kindly give some suggestions to overcome the problem.
Activate before use
source /path/to/ambertools/lib/python3.x/site-packages/GMXMMPBSA/GMXMMPBSA.sh
Change path/to by your matching directory
Okay Sir. Problem is solved. Thank you so much.
could you please tell me how did you solve it ?
@@tanverhasan7059 activate gmx to use further just see in comments or on original website
when i start the test gmx_MMPBSA_test it shows
git failed when trying to clone the gmx_MMPBSA repository
plz help sir
Write command with sudo
And try with better internet connectivity.
Dear Sir
Thank you very much for this nice video. In the 4th step (gmx_MMPBSA_test), I got ERROR message in all the 9 steps. The message is:
Please, check the test log
(/home/techno84/gmx_MMPBSA_test/examples/Entropy_calculations/Interaction_Entropy/15.log)
I got this ERROR message in all the 9 steps.
Please can you help me? How can I fix this problem before proceeding to the running the gmx_mmpbsa?
First run this command
source /usr/local/gromacs/bin/GMXRC
Or
export CMAKE_PREFIX_PATH=/usr/local/gromacs
Then run the gmx test command.
@@chemvigyan8518 Dear professor, when installing gmx_MMPBSA it presented the same error mentioned above in all stages, I carried out the aforementioned suggestion, but the error persists. I'm using gromacs 2020.4, what should I do? Thank you if you can help!
Activate gromacs before testing
Sir can we use this tool if we used gromos 54a7 forcefield for protein and ligand
Amber, charmm and opls force field is only supported.
Sir...i am new to in silico approach to study ligand protein interaction....., I am facing issues with obtaining the .xtc, .trp, .ndx files for mmpbsa
No video tutorials or..any of the actual tutorials in mentioning how to obtain this filez
You have to perform md simulation first. Where you can get these file.
This step is after step of md simulation
@@sethupathiraj th-cam.com/play/PLX1Wyd5Apzm5XMY8R5fbnHy875zPxYGad.html
Watch this first
@@chemvigyan8518 thank you sir
Sir, I'm getting following error.
-Gromacs error: Structure contains JZ4 molecules, but no template defined.
Please Help.
Replace the lig word with JZ4 where it is being used
Sir when I replace the lig with JZ4 ...
Same error is coming: structure contains LIG molecules but no template defined
Also when i write other commands from the valdes website...
gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ci index.in -cg 1 13 -ct md_0_10_noPBC.xtc -lm JZ4.mol2 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_REDULTS_MMPBSA.cv
Error: parmchk2 failed when quering JZ4.mol2
@@shashianand paste your queries in gmx_mmpbsa email group for best assistance.
how should I solve this error: " QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-bioilgaz'
ERROR:root:MMPBSA_Error"
Use the centred xtc file and then check it again
@@chemvigyan8518 okay and now, once when i try to open the gui i get the following error:
"qt.qpa.xcb: could not connect to display"
how am i going to open du gui?
Okay I understood, GUI cannot be opened on LINUX WSL systems, therefore it is not a problem but it still gives the final results data
@@ilgaztastekil6633 ok
Thank you for your great video.
I had the following error when I was running "conda update conda" command:
CondaHTTPErrore: HTTP connection failed for url ...
What shall I do to get ride of this error?
run the command with better internet connectivity
@@chemvigyan8518 thank you very much, it really worked!
I did all the steps as you said, but unfortunately when I run "gmx_mmpbsa_test" command I had ERROR state for all kind of interactions: protein-protein, protein-ligand and ...
What's the reason. I ran all the previous commands successfully without errors!
24495 Bert Trafficway
Hello Sir
in my system ParmEd is not getting installed
Kindly tell me the way to install it
Follow this
github.com/conda-forge/parmed-feedstock
github.com/conda-forge/parmed-feedstock
Am using ubuntu by the last command where the is in need does not work would you pls help me
Send me the screenshot of the error
Ok
I sent it to you would you please help me sir thank you
Sir how to remove the (base) command in ubuntu
Create an environment
Then activate that environment
that github page is not found how to install now
github.com/Valdes-Tresanco-MS/gmx_MMPBSA
@@chemvigyan8518 I have completed all the steps sir but i cant install the parmed and the mmpbsa test was failed
Can we launch xserver to import gmx_mmpbsa_ana
I've used it to import XMgrace on windows subsystem for linux
@@chemistryforall-bynsridhara yes you can use it.
sir, how to plot a graph please sir upload a video
Ok I forgoted
Send the files again to make the group which you send me earlier. I missed them.
X-score software
CDRUG
FAF Drug 4 server
Cell line cytotoxicity pred.
Ok in Saturday Sunday I will do
Thank you sir, i will be wait for these videos 😍😍
Please make these videos on hindi+English=Hinglish language...
@@surajjoshi3612 ok
@@chemvigyan8518 Thanku sir
Hi sir pls help me
sir, when i go to test the gmx_MMPBSA_test command then such type of error shows
[INFO ] Cloning gmx_MMPBSA repository in /home/jai123/gmx_MMPBSA_test
Cloning into '/home/jai123/gmx_MMPBSA_test'...
remote: Enumerating objects: 21565, done.
remote: Counting objects: 100% (2397/2397), done.
remote: Compressing objects: 100% (566/566), done.
remote: Total 21565 (delta 1401), reused 2322 (delta 1343), pack-reused 19168
Receiving objects: 100% (21565/21565), 334.86 MiB | 4.22 MiB/s, done.
Resolving deltas: 100% (14954/14954), done.
Updating files: 100% (697/697), done.
[INFO ] Cloning gmx_MMPBSA repository...Done.
[INFO ] Example STATE
--------------------------------------------------------------------------------
[INFO ] Protein-Ligand (Single trajectory approximation) RUNNING
[ERROR ] Protein-Ligand (Single trajectory approximation) [ 1/ 9] ERROR
Please, check the test log
(/home/jai123/gmx_MMPBSA_test/examples/Protein_ligand/ST/3.log)
[INFO ] Protein-Protein RUNNING
[ERROR ] Protein-Protein [ 2/ 9] ERROR
Please, check the test log
(/home/jai123/gmx_MMPBSA_test/examples/Protein_protein/4.log)
[INFO ] Protein-DNA RUNNING
[ERROR ] Protein-DNA [ 3/ 9] ERROR
Please, check the test log
(/home/jai123/gmx_MMPBSA_test/examples/Protein_DNA/5.log)
[INFO ] Protein-Glycan RUNNING
[ERROR ] Protein-Glycan [ 4/ 9] ERROR
Please, check the test log
(/home/jai123/gmx_MMPBSA_test/examples/Protein_glycan/7.log)
[INFO ] Comp_receptor RUNNING
[ERROR ] Comp_receptor [ 5/ 9] ERROR
Please, check the test log
(/home/jai123/gmx_MMPBSA_test/examples/Comp_receptor/9.log)
[INFO ] Alanine Scanning RUNNING
[ERROR ] Alanine Scanning [ 6/ 9] ERROR
Please, check the test log
(/home/jai123/gmx_MMPBSA_test/examples/Alanine_scanning/12.log)
[INFO ] Stability calculation RUNNING
[ERROR ] Stability calculation [ 7/ 9] ERROR
Please, check the test log
(/home/jai123/gmx_MMPBSA_test/examples/Stability/13.log)
[INFO ] Decomposition Analysis RUNNING
[ERROR ] Decomposition Analysis [ 8/ 9] ERROR
Please, check the test log
(/home/jai123/gmx_MMPBSA_test/examples/Decomposition_analysis/14.log)
[INFO ] Interaction Entropy approximation RUNNING
[ERROR ] Interaction Entropy approximation [ 9/ 9] ERROR
Please, check the test log
(/home/jai123/gmx_MMPBSA_test/examples/Entropy_calculations/Interaction_Entropy/15.log)
Export gromacs before running the text
@@chemvigyan8518 thank you sir
Thank you sir
Hello sir whn ever I try to run gmxMMPSA command it shows a gromacs error "Structure contains LIG molecules, but no template defined". Can you please tell me how to solve this
Make sure your working directory contains lg.itp or ligand.itp.
@@chemvigyan8518 Yes ir the ITP file is present but it still showing error
@@user-zu4yz5yt4l what is name of this life.itp or ligand.itp
@@chemvigyan8518 LIG.itp
Thank you sir