v1.6.1 Error Gromacs

[laodeaman-ai]

Hello Sir...

I hope you are doing great

I am encountering an error when executing the following command using gmx_MMPBSA version 1.6.1 on Ubuntu 20.04 with gmx 2022.5 and ambertools21.12:

gmx_MMPBSA -O -i gb.in -cs ../md.tpr -ct ../md.xtc -ci ../index.ndx -cg 1 13 -cp ../topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

After running the above command, I receive the following error message:

[INFO ] Checking gb.in input file... [INFO ] Checking gb.in input file...Done.

[INFO ] Checking external programs... [INFO ] cpptraj found! Using /home/arga/miniconda3/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /home/arga/miniconda3/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /home/arga/miniconda3/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /home/arga/miniconda3/envs/gmxMMPBSA/bin/sander [INFO ] Using GROMACS version 4.x.x! [ERROR ] MMPBSA_Error

I would greatly appreciate any guidance or solution to resolve this error. Thank you for your assistance.

[Valdes-Tresanco-MS]

Please, attach the gmx_MMPBSA.log file

[laodeaman-ai]

This is the log file content: [INFO ] Starting gmx_MMPBSA v1.6.1 [DEBUG ] WDIR : /home/arga/Downloads/lig0_5fu_egfr/gb [DEBUG ] AMBERHOME : /home/arga/miniconda3/envs/gmxMMPBSA [DEBUG ] PYTHON EXE : /home/arga/miniconda3/envs/gmxMMPBSA/bin/python [DEBUG ] PYTHON VERSION: 3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 08:45:29) [GCC 10.4.0] [DEBUG ] MPI : /home/arga/miniconda3/envs/gmxMMPBSA/bin/mpirun [DEBUG ] ParmEd : 3.4.3+11.g41cc9ab [DEBUG ] OS PLATFORM : Linux-5.15.0-76-generic-x86_64-with-glibc2.31 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION : #83~20.04.1-Ubuntu SMP Wed Jun 21 20:23:31 UTC 2023 [DEBUG ] OS PROCESSOR : x86_64

[INFO ] Command-line gmx_MMPBSA -O -i gb.in -cs ../md.tpr -ct ../md.xtc -ci ../index.ndx -cg 1 13 -cp ../topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[DEBUG ] |Input file: [DEBUG ] |-------------------------------------------------------------- [DEBUG ] |Input file generated by gmx_MMPBSA (v1.6.1) [DEBUG ] |Be careful with the variables you modify, some can have severe consequences on the results you obtain. [DEBUG ] | [DEBUG ] |# General namelist variables [DEBUG ] |&general [DEBUG ] | sys_name = "GB" # System name [DEBUG ] | startframe = 1 # First frame to analyze [DEBUG ] | endframe = 9999999 # Last frame to analyze [DEBUG ] | interval = 1 # Number of frames between adjacent frames analyzed [DEBUG ] | forcefields = "oldff/leaprc.ff99SB,leaprc.gaff" # Define the force field to build the Amber topology [DEBUG ] | ions_parameters = 1 # Define ions parameters to build the Amber topology [DEBUG ] | PBRadii = 3 # Define PBRadii to build amber topology from GROMACS files [DEBUG ] | temperature = 298.15 # Temperature [DEBUG ] | qh_entropy = 0 # Do quasi-harmonic calculation [DEBUG ] | interaction_entropy = 0 # Do Interaction Entropy calculation [DEBUG ] | ie_segment = 25 # Trajectory segment to calculate interaction entropy [DEBUG ] | c2_entropy = 0 # Do C2 Entropy calculation [DEBUG ] | assign_chainID = 0 # Assign chains ID [DEBUG ] | exp_ki = 0.0 # Experimental Ki in nM [DEBUG ] | full_traj = 0 # Print a full traj. AND the thread trajectories [DEBUG ] | gmx_path = "gmx" # Force to use this path to get GROMACS executable [DEBUG ] | keep_files = 2 # How many files to keep after successful completion [DEBUG ] | netcdf = 0 # Use NetCDF intermediate trajectories [DEBUG ] | solvated_trajectory = 1 # Define if it is necessary to cleanup the trajectories [DEBUG ] | verbose = 1 # How many energy terms to print in the final output [DEBUG ] |/ [DEBUG ] | [DEBUG ] |# (AMBER) Generalized-Born namelist variables [DEBUG ] |&gb [DEBUG ] | igb = 5 # GB model to use [DEBUG ] | intdiel = 1.0 # Internal dielectric constant for sander [DEBUG ] | extdiel = 78.5 # External dielectric constant for sander [DEBUG ] | saltcon = 0.0 # Salt concentration (M) [DEBUG ] | surften = 0.0072 # Surface tension [DEBUG ] | surfoff = 0.0 # Surface tension offset [DEBUG ] | molsurf = 0 # Use Connelly surface ('molsurf' program) [DEBUG ] | msoffset = 0.0 # Offset for molsurf calculation [DEBUG ] | probe = 1.4 # Solvent probe radius for surface area calc [DEBUG ] | ifqnt = 0 # Use QM on part of the system [DEBUG ] | qm_theory = "" # Semi-empirical QM theory to use [DEBUG ] | qm_residues = "" # Residues to treat with QM [DEBUG ] | qmcharge_com = 0 # Charge of QM region in complex [DEBUG ] | qmcharge_lig = 0 # Charge of QM region in ligand [DEBUG ] | qmcharge_rec = 0 # Charge of QM region in receptor [DEBUG ] | qmcut = 9999.0 # Cutoff in the QM region [DEBUG ] | scfconv = 1e-08 # Convergence criteria for the SCF calculation, in kcal/mol [DEBUG ] | peptide_corr = 0 # Apply MM correction to peptide linkages [DEBUG ] | writepdb = 1 # Write a PDB file of the selected QM region [DEBUG ] | verbosity = 0 # Controls the verbosity of QM/MM related output [DEBUG ] | alpb = 0 # Use Analytical Linearized Poisson-Boltzmann (ALPB) [DEBUG ] | arad_method = 1 # Selected method to estimate the effective electrostatic size [DEBUG ] |/ [DEBUG ] | [DEBUG ] |# Decomposition namelist variables [DEBUG ] |&decomposition [DEBUG ] | idecomp = 2 # Which type of decomposition analysis to do [DEBUG ] | dec_verbose = 0 # Control energy terms are printed to the output [DEBUG ] | print_res = "within 6" # Which residues to print decomposition data for [DEBUG ] | csv_format = 1 # Write decomposition data in CSV format [DEBUG ] |/ [DEBUG ] | [DEBUG ] |-------------------------------------------------------------- [DEBUG ] [INFO ] Checking gb.in input file... [INFO ] Checking gb.in input file...Done.

[INFO ] Checking external programs... [INFO ] cpptraj found! Using /home/arga/miniconda3/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /home/arga/miniconda3/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /home/arga/miniconda3/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /home/arga/miniconda3/envs/gmxMMPBSA/bin/sander [INFO ] Using GROMACS version 4.x.x! [ERROR ] MMPBSA_Error

Could not find necessary program [ GROMACS ]

Check the gmx_MMPBSA.log file to report the problem.

[Valdes-Tresanco-MS]

You must have a gromacs executable in the PATH. You can install it from conda as follows:

conda install -c conda-forge gromacs -y -q

[laodeaman-ai]

Hello,

I followed the suggestion provided and attempted to install GROMACS using the command "conda install -c conda-forge gromacs -y -q". Prior to that, I deactivated the PATH in .bashrc of the previously installed GROMACS version. However, I am still encountering the same error. I have attached a screenshot and the log file for reference.

Could you please provide further assistance to resolve this issue? Your help is greatly appreciated.

Thank you. gmx_MMPBSA.log

[Valdes-Tresanco-MS]

But you installed gromacs in the base environment, not on the gmxMMPBSA one. Please, activate the gmxMMPBSA environment, install gromacs, and check if it exists.