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dptech-corp / Uni-GBSA

An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.
Apache License 2.0
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I would like to simplify the file preparation for MD with unigbsa. What should I do? #56

Open Tangbbmc opened 1 week ago

Tangbbmc commented 1 week ago

It is well-known that preparing the files for molecular dynamic (MD) simulation of protein-ligand complex is a tedious process, which includes preparing ligand topology, solvation, adding ions, energy minimization, equilibration, and so on. Could I simplify the file preparation for 100-ns gromacs MD run of one protein-ligand complex with unigbsa?

Aunity commented 1 day ago

Yes, you can just use the command unigbsa-md to do that, here is an example:

unigbsa-md -p 1ceb_protein.pdb -l 1ceb_ligand.sdf -pf amber99sb -lf gaff -bt cubic -d 1.0 -conc 0.15 -o md-100ns -nsteps 50000000 -nframe  10000 -nt 16