After successfully carrying out a 10ns MD simulation of a protein-ligand complex from gromacs, i use the files obtained from the final mdrun to calculate g_mmpbsa. However, the process is stuck at g_mmpbsa reading md_0_10.tpr
The installation procedure followed was the first one at
https://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html
Can you make your question more clear or post a screenshot of your error?
" the process is stuck at g_mmpbsa reading md_0_10.tpr " struck???
what version of gromacs are you using? Perhaps that version of gromacs is not compatible with the version of g_mmpbsa.
check gmx_MMPBSA, a new tool aid to perform end-state free energy calculations with GROMACS files. Things you can do with gmx_MMPBSA:
-binding free energy with different solvation models (PB, GB, or MM/3D-RISM)
-stability
-alanine scanning
-entropy corrections
-binding free energy decomposition
gmx_MMPBSA has been written in Python3.8 and is entirely based on AMBER’s MMPBSA.py, a widely used tool for streamlining end-state free energy calculations. The program is freely available (test files and tutorials included) at https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA
hth!
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