Closed nonsensejoke closed 1 month ago
The ligand is probably too large (56 atoms) for ABFE. The perturbation energy distributions (see Rplots.pdf) are disconnected. I recommend binding a fragment of the ligand first and then use RBFE to progressively build the full ligand. See https://pubs.rsc.org/en/content/articlelanding/2023/cp/d3cp02125d for an example.
I also recommend double-checking the location of the binding site region (the LIGAND_CM_ATOMS, RCPT_CM_ATOMS, CM_KF, and CM_TOL settings) to confirm that it is consistent with the desired binding pose.
Thank you very much for your suggestion and the paper. I will look into this.
Hello Professor Gallicchio,
I tried to run ABFE simulation with AToM for a protein+ligand system built with my own tool chain. I first obtained AMBER prm7/rst7 files, then convert them into xml/pdb files for OpenMM.
I tried several ligands against the same receptor protein and found that all my ABFE results are positive (I expect negative values as the ABFE examples). I wonder what the cause can be in this situation.
In the zip file below, I have attached the
cntl
file,uwham_analysis
input/output, theanalyze.sh
script and Rplots.pdf. atom-abfe-result.zipThank you for your time.