Hi everyone,
I am trying to calculate MM-PBSA or MM-GBSA for ligand-protein structures in my simulations with GROMACS 2020.5. version. There are recommended calculations for older versions of GROMACS, but are there any calculation methods you can recommend for recent versions?
Ekrem Yaşar have a go with gmx_MMPBSA, compatible with all GROMACS versions
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/getting-started/
see all the examples here:
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/
As far as I know all GROMACS versions for gmx_MMPBSA should work with AmberTools. Hopefully without AmberTools we can have a calculation that works only in the GROMACS later. Actually, for the simulations produced with Amber, I make these calculations using AmberTools, but I will try to use the gmx_MMPBSA you recommended for the GROMACS simulations. Thanks for your advice Mario E. Valdés-Tresanco.
gmx_MMPBSA offers way more options than other programs designed to work with GROMACS files:
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/versus/
The fact that gmx_MMPBSA depends on AmberTools is not an issue by any means. gmx_MMPBSA can be installed in an isolated conda environment along with its dependencies.
We chose AmberTools since programs to perform end-point free energy calculations in AmberTools are very well-tested and well-acknowledged by the community. gmx_MMPBSA brings these advantages to the GROMACS community.
Mario E. Valdés-Tresanco After completing the installation of gmx_MMPBSA with Ambertools21 on macos, I ran it and that is works for me. Obtained results are successful. Thank you for your help.
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