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 - 14:30:03 PST
