Recently, I did MD simulations using online tools. But I am not able to calculate the ligand binding energy of my complexes. So, how I can calculate the ligand binding energy of a complex by using MM-GBSA or MM-PBSA approach?
Waseem Ahmad Ansari
Jyoti Sankar Prusty You have to do through AMBER, GROMACS, DS(Discovery studio CDOCKER), Schrodinger PRIME, NAMD etc.
0 votes
0 thanks
Sun Tiedong
Why not start with some googling? for example http://ambermd.org/tutorials/advanced/tutorial3/
0 votes
0 thanks
Kandhan Palanisamy
Jyoti Sankar Prusty You may try with g_mmpbsa.
https://rashmikumari.github.io/g_mmpbsa/Tutorial.html
Or
MM-PBSA and MM-GBSA methods in AMBER.
https://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.php
1 votes
0 thanks
Mario E. Valdés-Tresanco
try gmx_MMPBSA
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/getting-started/
0 votes
0 thanks
- Badges
- Science topic
More Jyoti Sankar Prusty's questions See All
Similar questions and discussions