Re: Positive Binding Free energy in CHARMM27

[Mario Ernesto]

Usually for systems prepared with charmm force field is recommended to use PB instead of GB... also, if the binding site contains a high number of charged amino acids, consider using a higher dielectric constant...

hope this helps!

El mié, 11 may 2022 a las 20:49, Lucas Lima (<lucas...@gmail.com>) escribió:

Good evening,

The MMPBSA results showed the binding free energy-positive values. However, I am looking for the reason for this; however,  the positive value is persisting.
The commands utilized were these:
1) gmx trjconv -s md.tpr -f md.xtc -pbc mol -ur compact -center -b 90000 -e 100000 -o md_nopbc.xtc
Obs: I choose the protein (Group 1) and the system for the output (Group 0)

2) gmx trjconv -s md.tpr -f md_nopbc.xtc -o md_fit.xtc -fit rot+trans -b 90000 -e 100000
Obs: I choose the protein (Group 1) and the system for the output (Group 0)

3)  gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ct md_fit.xtc -cg 1 13 -cp topol.top  -ci index_complex.ndx
Obs: In index_complex.ndx file, I joined the protein with the ligand using the command below: gmx make_ndx -f md.gro -o index_complex.ndx
1 | 13
obs: Group 1 is the protein and the group 13 is the ligand.

Below are the files generated by mmpbsa with positive values
Obs: I am simulating the protein-ligand system with the 100 ns!

Greets!

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