I have run a simulation in gromacs 2020.4 and am unable to perform mmpbsa due to version mismatch in tpr file.
Can I use Tpr file prepared in gromacs 5.1 along with .xtc file from gromacs 2020.4?
Will it give correct results?
Is there any other method to do mmpbsa calculation using gromacs 2020.4 data?
Dwaipayan Chaudhuri give it a try to gmx_MMPBSA (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/getting-started/). It works with all GROMACS versions along with AmberTools20 or 21.
There are many options for running gmx_MMPBSA. Among the types of calculations you can do are:
- Normal binding free energies
- Stability
- Alanine scanning
- Entropy corrections
- Decomposition schemes
- QM/MMGBSA
hth!
No, you can't use tpr or any other binary format files (xtc, trr) prepared in one gromacs version and then run it in a different one. Text files (gro, ndx, topology and so on) are, however, fine.
If you have two different versions of gromacs you can prepare the final gro file together with topology and index files in any version, but to create the tpr file (using gmx grompp) you have to use the same version as you will run the simulation (using gmx mdrun).
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