Looks like your prmtop files were not created properly since your atom numbers don’t match between the netcdf and complex prmtop. Did you use ante-MMPBSA.py to create your dry complex, receptor, and ligand prmtop files? If so, could you post the command you used? Can I assume at least one of your ligands has 29 atoms (this missing atoms 1838-1809)?
Also, is there any chance your two ligands are the same and given the same residue name in Amber? That would make generating the prmtop files a little more difficult, but still possible (I’ve done it actually).
-Bill
> On Dec 7, 2022, at 4:11 PM, laura zhang via AMBER <amber.ambermd.org> wrote:
>
> Dear all,
>
> I conducted an amber simulation which includes one protein and two ligands. I want to calculate the binding free energy of the protein with the 2nd ligand. I have the code to calculate mmgbsa energy pasted below.
>
> solv_parm="./tm2.wet.complex.parm7"
> complex_parm="./tm2.gas.comp2.parm7"
> receptor_parm="./tm2.gas.receptor.parm7"
> lig_parm="./tm2.gas.lg2.parm7"
> trajectory="./10.prod.trj"
> MMPBSA.py -O -i mmbgsa.in \
> -o tm2_mmgbsa_results_10.dat \
> -eo tm2_mmgbsa_perframe_10.dat \
> -sp ${solv_parm} \
> -cp ${complex_parm} \
> -rp ${receptor_parm} \
> -lp ${lig_parm} \
> -y ${trajectory}
>
> here, complex includes receptor+lg1+lg2 (1838 atoms), while comp2 includes receptor+lg2 (1809 atoms), and tm2.wet.complex.parm7 file can load 10.prod.trj file using vmd program.
>
> I got the error message in the log file as "Error: Number of atoms in NetCDF file (1838) does not match number
> Error: in associated topology (1809)!
> Error: Could not set up '_MMPBSA_complex.nc.0' for reading.
> Error: Could not set up input trajectory '_MMPBSA_complex.nc.0'.
>
> I am wondering how to solve such kind of problem. Thank you very much.
>
> Laura
>
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Received on Wed Dec 07 2022 - 15:00:03 PST
