I have simulated a protein-ligand complex by using gromacs software and gromos 54A7 force field was deployed for this purpose. Ligand topology (.itp) file was prepared by usimg ATB server. Now my questin is that can I use single trajectory method of gmx_MMPBSA tool to calculate protein-ligand binding free energy?
yes, it is very convenient to calculate binding energy between protein and ligand via mmpbsa
Hi,
for GROMOS it's a no-go, gmx_MMPBSA is more adapted for AMBER forcefields. Try g_mmpbsa instead.
Ricardo J Ferreira Thank you for your valuable advice.
I have tried g_mmpbsa but its was showing Segmentation fault (core dumped). In internet I have checked. And not getting any clue by which I can solve this problem. I have tried with several computers with large RAM. So it's clear for me that it's not a memory problem
Madhusudan Dutta Ricardo J Ferreira There is an indirect way to use gmxMMPBSA for systems simulated using gromos FF's.
The trajectories from gromos simulations can be spliited into multiple pdbs (as per analysis requirements) and again converted to OPLSAA format using pdb2gmx module. The OPLSAA formatted pdbs can now be procesed by gmxMMPBSA. Thanks!
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