Closed debanjansen48 closed 4 months ago
I think i need to install it using amber.python method. I installed it in one of my lab computer with Gromacs 2024.1 and working.
But when i am trying to install it in my workstation returns following error. weher as amber.sh path sourced and tleap working.
base) debanjan@debanjan:~/Desktop$ source /home/debanjan/amber22/amber.sh
(base) debanjan@debanjan:~/Desktop$ gmx_MMPBSA
Traceback (most recent call last):
File "/home/debanjan/amber22/miniconda/lib/python3.10/site-packages/GMXMMPBSA/app.py", line 27, in
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/debanjan/amber22/miniconda/bin/gmx_MMPBSA", line 5, in
@debanjansen48 probably the first error is related to the gromacs
version. Maybe you want to define the gmx executable you used for the MD through the gmx_path
variable in the input file.
the second one is probably related to the pandas
version. We recommend using the conda env because you can take more control over the dependencies version. The latest versions of gmx_MMPBSA hasn't been tested using the standalone Ambertools installation
if i use conda env it can not execute gromacs 2024 trajectory sir
how to modify pandas
if i use conda env it can not execute gromacs 2024 trajectory sir
You can use a custom gromacs executable defining it in thegmx_path
variable in the input file
thank you, its now working with all vertions..
outcome
Bug summary
When running for other complex its working for few system not working giving following error.
I run some MD simulation with Gromacs 2023 for them its working. The md simulation executed with Gromacs 2024 for them getting following err.
Terminal output
gmx_MMPBSA.log
[INFO ] Starting gmx_MMPBSA v1.6.1 [DEBUG ] WDIR : /media/debanjan/DS-1TB/Project/PhD_Students/Shovan/5ZZV/Md/3/MMGBSA [DEBUG ] AMBERHOME : /home/debanjan/miniconda3/envs/gmxMMPBSA [DEBUG ] PYTHON EXE : /home/debanjan/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/debanjan/MPICH4/bin/mpirun [DEBUG ] ParmEd : 3.4.3+11.g41cc9ab [DEBUG ] OS PLATFORM : Linux-5.15.0-102-generic-x86_64-with-glibc2.35 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION : #112-Ubuntu SMP Tue Mar 5 16:50:32 UTC 2024 [DEBUG ] OS PROCESSOR : x86_64
[INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs ../md_100.tpr -ct ../md_100.xtc -ci index.ndx -cg 1 13 -cp ../topol.top -o 3_RESULTS_MMPBSA.dat -eo 3_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 = "Lig-2" # System name [DEBUG ] | startframe = 1 # First frame to analyze [DEBUG ] | endframe = 9999999 # Last frame to analyze [DEBUG ] | interval = 1000 # 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 = 300 # 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 = "" # 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 ] |-------------------------------------------------------------- [DEBUG ] [INFO ] Checking mmpbsa.in input file... [INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs... [INFO ] cpptraj found! Using /home/debanjan/miniconda3/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /home/debanjan/miniconda3/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /home/debanjan/miniconda3/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /home/debanjan/miniconda3/envs/gmxMMPBSA/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /home/debanjan/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [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... [DEBUG ] Running command: echo -e "name 1 GMXMMPBSA_REC\n name 13 GMXMMPBSA_LIG\n 1 | 13\n q\n" | /home/debanjan/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f ../md_100.tpr [DEBUG ] :-) GROMACS - gmx make_ndx, 2022.4-conda_forge (-: [DEBUG ] [DEBUG ] Executable: /home/debanjan/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/debanjan/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /media/debanjan/DS-1TB/Project/PhD_Students/Shovan/5ZZV/Md/3/MMGBSA [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f ../md_100.tpr [DEBUG ] [DEBUG ] [DEBUG ] Reading structure file [DEBUG ] Reading file ../md_100.tpr, VERSION 2024.1 (single precision) [DEBUG ] Reading file ../md_100.tpr, VERSION 2024.1 (single precision) [ERROR ] MMPBSA_Error
/home/debanjan/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx failed when querying index.ndx
Check the gmx_MMPBSA.log file to report the problem.
Operating system
Linux Mint
gmx_MMPBSA Version
v1.6.1
Python version
Python 3.9.15
Installation
conda AmberTools + pip