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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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Difficulty to install gmx-mmpbsa #122

Closed srdjan125 closed 2 years ago

srdjan125 commented 2 years ago

Hello,

I have tried to install the gmx-mmpbsa program today. First I have installed Ambertools by conda command, then mpirun (which I already have), then I have tried to test if program is working by downloading files from "protein-protein tutorial" , however after typing command: gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 19 20 -ct com_traj.xtc

I get the following error:

Traceback (most recent call last): File "/home/srdjan/anaconda3/lib/python3.7/site-packages/GMXMMPBSA/app.py", line 26, in from GMXMMPBSA import main File "/home/srdjan/anaconda3/lib/python3.7/site-packages/GMXMMPBSA/main.py", line 38, in from GMXMMPBSA.createinput import create_inputs File "/home/srdjan/anaconda3/lib/python3.7/site-packages/GMXMMPBSA/createinput.py", line 43, in from parmed.amber.mdin import Mdin ModuleNotFoundError: No module named 'parmed'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/srdjan/anaconda3/bin/gmx_MMPBSA", line 5, in from GMXMMPBSA.app import gmxmmpbsa File "/home/srdjan/anaconda3/lib/python3.7/site-packages/GMXMMPBSA/app.py", line 35, in (amberhome, amberhome)) (base) srdjan@srdjan-HP-ProDesk-400-G4-SFF:~/Desktop/gmx-MMPBSA/Tutorial/Protein_protein$ conda activate AmberTools21 (AmberTools21) srdjan@srdjan-HP-ProDesk-400-G4-SFF:~/Desktop/gmx-MMPBSA/Tutorial/Protein_protein$ gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 19 20 -ct com_traj.xtc gmx_MMPBSA: command not found

If I tried to run the same command by activating AmberTools20 (AmberTools21) environment, I get that gmx-mmpbsa command does not exist.

I would appreciate if someone could help me with this.

Valdes-Tresanco-MS commented 2 years ago

Did you install AmberTools following the instructions on the Amber website? If so, then it is normal that both are not in the same environment. The gmx_MMPBSA installation instructions are based on the AmberTools compilation. The gmx_MMPBSA installation procedure, assuming you will install AmberTools as described on the Amber website, would be as follows: conda create --name AmberTools21 conda activate AmberTools21 conda install -c conda-forge mpi4py ambertools=21 compilers python -m pip install PyQt5 gmx_MMPBSA

To use gmx_MMPBSA you must always activate this environment

srdjan125 commented 2 years ago

Hello,

Thank you for help, now it is working. I was also trying something similar but with AmberTools20 (because I thought that I needto have AmberTools20) and it did not work.

Greetings.

From: Mario Sergio Valdés Tresanco @.> Sent: Tuesday, January 18, 2022 7:33 PM To: Valdes-Tresanco-MS/gmx_MMPBSA @.> Cc: srdjan125 @.>; Author @.> Subject: Re: [Valdes-Tresanco-MS/gmx_MMPBSA] Difficulty to install gmx-mmpbsa (Issue #122)

Did you install AmberTools following the instructions on the Amber website? If so, then it is normal that both are not in the same environment. The gmx_MMPBSA installation instructions are based on the AmberTools compilation. The gmx_MMPBSA installation procedure, assuming you will install AmberTools as described on the Amber website, would be as follows: conda create --name AmberTools21 conda activate AmberTools21 conda install -c conda-forge mpi4py ambertools=21 compilers python -m pip install PyQt5 gmx_MMPBSA

To use gmx_MMPBSA you must always activate this environment

— Reply to this email directly, view it on GitHubhttps://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/122#issuecomment-1015698466, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUJN6QITCAVMVWMV3N46LQLUWWXBFANCNFSM5MHZA4GQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you authored the thread.Message ID: @.***>

Valdes-Tresanco-MS commented 2 years ago

gmx_MMPBSA is compatible with both the compiled version of ambertools20 and the conda versions (ambertools21). Currently, we have a conda package that installs all the dependencies, so we'll be updating the documentation soon. Cheers! Mario S.

srdjan125 commented 2 years ago

Hello,

May I ask again for help.

I have run Generalized Born calculations for protein-protein system by opton:

gmx_MMPBSA -O -i mmpbsa.in -cs Check.tpr -ci ind3.ndx -cg 19 20 -ct CheckB.xtc -cp topol1.top -cr First.pdb

At the end of calculations, gmx_ana givrs me only bar plots of final/average energies for complex, protein1, protein and delta.

However, I want to see also plots of time evolution (for example VdW versus simulation time), but I cannot get it. In tutorials I can see that gmx_ana can give also those plots and I could export data I want into csv file.

 May I ask what is the issue?  Maybe I do not start calculation with right command?

From: Mario Sergio Valdés Tresanco @.> Sent: Wednesday, January 19, 2022 11:44 AM To: Valdes-Tresanco-MS/gmx_MMPBSA @.> Cc: srdjan125 @.>; Author @.> Subject: Re: [Valdes-Tresanco-MS/gmx_MMPBSA] Difficulty to install gmx-mmpbsa (Issue #122)

gmx_MMPBSA is compatible with both the compiled version of ambertools20 and the conda versions (ambertools21). Currently, we have a conda package that installs all the dependencies, so we'll be updating the documentation soon. Cheers! Mario S.

— Reply to this email directly, view it on GitHubhttps://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/122#issuecomment-1016309104, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUJN6QIRM4N5H7MXV6552KLUW2I2VANCNFSM5MHZA4GQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you authored the thread.Message ID: @.***>

marioernestovaldes commented 2 years ago

Check these two videos

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/analyzer/#binding-free-energy-calculation-gb-ie

And

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/analyzer/#functionalities

Cheers!

srdjan125 commented 2 years ago

Thank you 🙂 . I did not notice that I can click on delta/complex and it will give me more options to plot VdW, EL etc. I also saw that I can write it into csv file at the end calculation by adding option -eo File_name.csv

Greetings.

From: Mario E. Valdés-Tresanco @.> Sent: Wednesday, January 19, 2022 7:30 PM To: Valdes-Tresanco-MS/gmx_MMPBSA @.> Cc: srdjan125 @.>; Author @.> Subject: Re: [Valdes-Tresanco-MS/gmx_MMPBSA] Difficulty to install gmx-mmpbsa (Issue #122)

Check these two videos

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/analyzer/#binding-free-energy-calculation-gb-ie

And

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/analyzer/#functionalities

Cheers!

— Reply to this email directly, view it on GitHubhttps://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/122#issuecomment-1016750737, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUJN6QLTMGMKQXXHTMO6OC3UW37LHANCNFSM5MHZA4GQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you authored the thread.Message ID: @.***>