search

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
216 stars 64 forks source link

[Question]: Running gmx_MMPBSA on my protein-protein system #146

Closed Surabhi-CSB closed 2 years ago

Surabhi-CSB commented 2 years ago

My Question is...

Hi,

I am using gmx_MMPBSA for analyzing my protein-protein system. I have gmx_MMPBSA version 2.1.2 installed.

The command I am using:

gmx_MMPBSA -O -i mmpbsa_interaction.in -cs md.tpr -ci index1.ndx -cg 23 31 -ct concatenated_cluster_compact_center_fitted_nowater_5us_dt1000_N-D_original.xtc -eo Energy_terms_N-D_Run1_dt1000.csv

The error I am getting is as follows:

[INFO ] Started [INFO ] Loading and checking parameter files for compatibility...

[INFO ] Checking external programs... [INFO ] cpptraj found! Using /home/surabhi/anaconda3/envs/pbsa2/bin/cpptraj [INFO ] tleap found! Using /home/surabhi/anaconda3/envs/pbsa2/bin/tleap [INFO ] parmchk2 found! Using /home/surabhi/anaconda3/envs/pbsa2/bin/parmchk2 [INFO ] mmpbsa_py_energy found! Using /home/surabhi/anaconda3/envs/pbsa2/bin/mmpbsa_py_energy [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /usr/local/bin/gmx [INFO ] Checking external programs...Done.

[INFO ] Building AMBER Topologies from GROMACS files... [INFO ] Checking if supported force fields exists in Amber data... [INFO ] Get PDB files from GROMACS structures files... [INFO ] Making gmx_MMPBSA index for complex... [INFO ] Normal Complex: Saving group 23_31 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [INFO ] No receptor structure file was defined. Using ST approach... [INFO ] Using receptor structure from complex to generate AMBER topology [INFO ] Normal Complex: Saving group 23 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [INFO ] No ligand structure file was defined. Using ST approach... [INFO ] Using ligand structure from complex to generate AMBER topology [INFO ] Normal ligand: Saving group 31 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [INFO ] Generating AMBER Compatible PDB Files... [INFO ] Building Tleap input files... [ERROR ] /home/surabhi/anaconda3/envs/pbsa2/bin/tleap failed when querying _GMXMMPBSA_leap.in File "/home/surabhi/anaconda3/envs/pbsa2/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/home/surabhi/anaconda3/envs/pbsa2/lib/python3.6/site-packages/GMXMMPBSA/app.py", line 111, in gmxmmpbsa app.loadcheck_prmtops() File "/home/surabhi/anaconda3/envs/pbsa2/lib/python3.6/site-packages/GMXMMPBSA/main.py", line 588, in loadcheck_prmtops FILES.mutant_receptor_prmtop, FILES.mutant_ligand_prmtop) = maketop.buildTopology() File "/home/surabhi/anaconda3/envs/pbsa2/lib/python3.6/site-packages/GMXMMPBSA/make_top.py", line 127, in buildTopology tops = self.makeToptleap() File "/home/surabhi/anaconda3/envs/pbsa2/lib/python3.6/site-packages/GMXMMPBSA/make_top.py", line 1082, in makeToptleap GMXMMPBSA_ERROR('%s failed when querying %s' % (tleap, self.FILES.prefix + 'leap.in')) File "/home/surabhi/anaconda3/envs/pbsa2/lib/python3.6/site-packages/GMXMMPBSA/exceptions.py", line 170, in init raise exc(msg + ' Check the gmx_MMPBSA.log file to report the problem.') MMPBSA_Error: /home/surabhi/anaconda3/envs/pbsa2/bin/tleap failed when querying _GMXMMPBSA_leap.in Check the gmx_MMPBSA.log file to report the problem. Exiting. All files have been retained.

The mmpbsa_interaction.in file used is as follows:

Sample input file for entropy calculations (IE) This input file is meant to show only that gmx_MMPBSA works. Althought, we tried to used the input files as recommended in the Amber manual, some parameters have been changed to perform more expensive calculations in a reasonable amount of time. Feel free to change the parameters according to what is better for your system.

&general startframe=1, endframe=5000, protein_forcefield="oplsaa.ff/forcefield.itp",

Interaction Entropy (IE)(https://pubs.acs.org/doi/abs/10.1021/jacs.6b02682) approximation

entropy=1, entropy_seg=25, entropy_temp=298 / &gb igb=2, saltcon=0.150, / ~

marioernestovaldes commented 2 years ago

Hi there! I see you are using opls force field... Unfortunately, at the moment gmx_MMPBSA doesnt have support for this force field, only for amber and charmm...

Cheers!

Surabhi-CSB commented 2 years ago

I have also tried using the "oldff/leaprc.ff99SB" as mentioned in the example file. However, it gives me the same error.

Valdes-Tresanco-MS commented 2 years ago

I have also tried using the "oldff/leaprc.ff99SB" as mentioned in the example file. However, it gives me the same error.

The force field used must be the same as the one used in the setup of the MD of your system . gmx_MMPBSA performs post-processing analysis, so you cannot change the default atom types and parameters for your system. At the moment, given the calculation engines it uses, gmx_MMPBSA does not support any system that is not explicitly prepared with AMBER or CHARMM force fields. In future versions, we will include other calculation engines that allow other force fields.

Mario S.

marioernestovaldes commented 2 years ago

@Surabhi-CSB support for OPLS force field has been added to gmx_MMPBSA... please, check this tutorial

hope this helps!

Surabhi-CSB commented 2 years ago

Hi,

Thank you so much for taking out time for this. I will check it out and let you know.

Regards, Surabhi

On Wed, Mar 9, 2022 at 12:52 PM Mario E. Valdés-Tresanco < @.***> wrote:

@Surabhi-CSB https://github.com/Surabhi-CSB support for OPLS force field has been added to gmx_MMPBSA... please, check this tutorial https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/OPLS/protein_protein/

hope this helps!

— Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/146#issuecomment-1062624580, or unsubscribe https://github.com/notifications/unsubscribe-auth/APRKNMO5UBVM7QUEMHJG3QLU7BGR3ANCNFSM5OUNVD6Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://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 were mentioned.Message ID: @.***>

-- Surabhi Rathore, SRF (DST-Inspire), C/o Dr. Lipi Thukral, Senior Scientist, CSIR-IGIB, Mathura Road, New Delhi-110025

LinkedIn Profile https://www.linkedin.com/in/surabhi-rathore-95bab6147/