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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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[Questunable to get the decomposition result #521

Closed suruchi-25 closed 1 month ago

suruchi-25 commented 1 month ago

My Question is...

i have completed the calculation by using the command gmx_MMPBSA -O -i mmpbsa.in -cs md_0_300.tpr -ct md_0_300_center150-300ns.xtc -ci index.ndx -cg 1 13 -cp topol.top -o LIG6_FINAL_RESULTS_MMPBSA.dat -eo LIG6_FINAL_RESULTS_MMPBSA.csv -do LIG6_FINAL_DECOMP_MMPBSA.dat -deo LIG6_FINAL_DECOMP_MMPBSA.csv but is not getting the lig6_final_decomp_mmpbsa.dat fine in the working directory. can someone help me out in knowing how to get the desired result?

Valdes-Tresanco-MS commented 1 month ago

You are overwriting the output file. Please, carefully read the documentation and the information of gmx_MMPBSA -h command

suruchi-25 commented 1 month ago

sorry, i am unable to understand what you want to say. how it can be checked?

Valdes-Tresanco-MS commented 1 month ago

Sorry, my mistake... Can you share the gmx_MMPBSA.log file and the output of ls in the working directory?

suruchi-25 commented 1 month ago

gmx_MMPBSA.log

gmx_MMPBSA -O -i mmpbsa.in -cs md_0_300.tpr -ct md_0_300_center150-300ns.xtc -ci index.ndx -cg 1 13 -cp topol.top -o LIG6_FINAL_RESULTS_MMPBSA.dat -eo LIG6_FINAL_RESULTS_MMPBSA.csv -do LIG6_FINAL_DECOMP_MMPBSA.dat -deo LIG6_FINAL_DECOMP_MMPBSA.csv

[[56362,1],0]: A high-performance Open MPI point-to-point messaging module was unable to find any relevant network interfaces:

Module: OpenFabrics (openib) Host: CUG

Another transport will be used instead, although this may result in lower performance.

NOTE: You can disable this warning by setting the MCA parameter btl_base_warn_component_unused to 0.

[INFO ] Starting gmx_MMPBSA v1.6.3 [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs md_0_300.tpr -ct md_0_300_center150-300ns.xtc -ci index.ndx -cg 1 13 -cp topol.top -o LIG6_FINAL_RESULTS_MMPBSA.dat -eo LIG6_FINAL_RESULTS_MMPBSA.csv -do LIG6_FINAL_DECOMP_MMPBSA.dat -deo LIG6_FINAL_DECOMP_MMPBSA.csv

[INFO ] Checking mmpbsa.in input file... [WARNING] &decomp namelist has not been defined in the input file. Ignoring '-deo' flag... [INFO ] Checking mmpbsa.in input file...Done.

[INFO ] Checking external programs... [INFO ] cpptraj found! Using /apps/codes/anaconda3/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /apps/codes/anaconda3/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /apps/codes/anaconda3/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /apps/codes/anaconda3/envs/gmxMMPBSA/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx_mpi found! Using /apps/codes/gromacs-2022/bin/gmx_mpi [INFO ] Checking external programs...Done.

[INFO ] Building AMBER topologies from GROMACS files... [INFO ] Get PDB files from GROMACS structures files... [INFO ] Making gmx_MMPBSA index for complex... [INFO ] Normal Complex: Saving group Protein_UNK (1_13) 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 Receptor: Saving group Protein (1) 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 UNK (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [INFO ] Checking the structures consistency... [INFO ] [INFO ] Using topology conversion. Setting radiopt = 0... [INFO ] Building Normal Complex Amber topology... [INFO ] Detected Amber/OPLS force field topology format... [WARNING] 14 invalid DIHEDRAL_PERIODICITY = 0 found in Complex topology... Setting DIHEDRAL_PERIODICITY = 1 [INFO ] Assigning PBRadii mbondi2 to Complex... [INFO ] Writing Normal Complex AMBER topology... [INFO ] No Receptor topology file was defined. Using ST approach... [INFO ] Building AMBER Receptor topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Receptor... [INFO ] Writing Normal Receptor AMBER topology... [INFO ] No Ligand topology file was defined. Using ST approach... [INFO ] Building AMBER Ligand topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Ligand... [INFO ] Writing Normal Ligand AMBER topology... [INFO ] Cleaning normal complex trajectories... [INFO ] Building AMBER topologies from GROMACS files... Done.

[INFO ] Loading and checking parameter files for compatibility... [INFO ] Preparing trajectories for simulation...

[INFO ] 10 frames were processed by cpptraj for use in calculation. [INFO ] Starting calculations in 1 CPUs...

[INFO ] Running calculations on normal system... [INFO ] Beginning GB calculations with /apps/codes/anaconda3/envs/gmxMMPBSA/bin/sander [INFO ] calculating complex contribution... 100%|######################| 10/10 [elapsed: 00:17 remaining: 00:00] [INFO ] calculating receptor contribution... 100%|######################| 10/10 [elapsed: 00:17 remaining: 00:00] [INFO ] calculating ligand contribution... 100%|######################| 10/10 [elapsed: 00:01 remaining: 00:00] [INFO ] Parsing results to output files...

[INFO ] Timing: [INFO ] Total GROMACS setup time: 12.950 sec. [INFO ] Total AMBER setup time: 0.723 sec. [INFO ] Creating trajectories with cpptraj: 0.254 sec. [INFO ] Total calculation time: 36.355 sec. [INFO ] Total GB calculation time: 33.424 sec. [INFO ] Statistics calculation & output writing: 0.018 sec. [INFO ] Total time taken: 50.323 sec.

[INFO ] Finalizing gmx_MMPBSA: [ERROR ] = 0; [WARNING] = 2 Check the gmx_MMPBSA.log file for more details...

[INFO ] Thank you for using gmx_MMPBSA. Please consider supporting gmx_MMPBSA by citing our publication: Valdés-Tresanco, M.S., Valdés-Tresanco, M.E., Valiente, P.A. and Moreno E. gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. J Chem Theory Comput., 2021, 17 (10):6281-6291. Epub 2021 Sep 29. PMID: 34586825. https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645

Also consider citing MMPBSA.py: Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke, H. and Roitberg, A. E. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. J. Chem. Theory Comput., 2012, 8 (9) pp 3314-3321

[INFO ] Opening gmx_MMPBSA_ana to analyze results...

[INFO ] Finalized...

Valdes-Tresanco-MS commented 1 month ago

According to the gmx_MMPBSA.log file you should get the output file in /home/suruchi/Desktop/S_3/CDK4/Lig6. Please, check if the file exist

ls | grep "LIG6_FINAL_RESULTS_MMPBSA.dat"
suruchi-25 commented 1 month ago

no file like this is obtained in the working directory