Hi everybody,
I'd appreciate any comments / help on the discrepancies shown below.
I run MMPBSA.py on the same 20ns trajectory twice.
1. Run 1
mpirun -np 12 MMPBSA.py.MPI -O -i mmpbsa.in -o RESULTS.dat -sp complex_solv.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y *.mdcrd
*.mdcrd represents 10x2ns trajectories
2. Run 2
Step 1. merge the 2ns trajectories into a 20ns.mdcrd while stripping waters and ions
Step 2. generated new topology files for complex, receptor and ligand
run MMPBSA.py
mpirun -np 12 MMPBSA.py.MPI -O -i mmpbsa.in -o RESULTS.dat -cp comp_new.prmtop -rp rec_new.prmtop -lp lig_new.prmtop -y *.mdcrd
Result of Run1.
DELTA G binding = -28.8956 +/- 2.8508 0.1275
Result of Run2
DELTA G binding = -26.5181 +/- 2.6507 0.3749
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Received on Wed Sep 28 2011 - 06:30:03 PDT
