I'm dealing with a protein-ligand complex in which I've preserved a water molecule closest to the ligand.
MMPBSA.py works fine for the calculation of Delta G and per residue energy decomposition.
However, an attempt to calculate the Entropy issues the following error message
$ mpirun -np 9 MMPBSA.py.MPI -O -i entropy.in -o FINAL_RESULTS_MMPBSA.dat -cp 2wch_bal.prmtop -rp 2wch.prmtop -lp bal.prmtop -y *.mdcrd > progress.log
Error: topology file solvated_prmtop does not exist!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
The entropy in file is:
Input file for running entropy calculations using NMode
&general
endframe=50, keep_files=2,
/
&nmode
nmstartframe=5, nmendframe=45,
nminterval=5, nmode_igb=1, nmode_istrng=0.1,
/
And the progress.log
MMPBSA.py.MPI being run on 9 processors
ptraj found! Using /Users/tzotzos/Programs/amber11/AmberTools/bin/ptraj
sander found! Using /Users/tzotzos/Programs/amber11/AmberTools/bin/sander
nmode program found! Using /Users/tzotzos/Programs/amber11/AmberTools/bin/mmpbsa_py_nabnmode
I'm not using a solvated_prmtop file as I've created new topologies after treating the complex for closest waters.
By the way, I did not use a solvated_prmtop for the calculation of Delta G, which as shown below runs smoothly
$ mpirun -np 12 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp 2wch_bal.prmtop -rp 2wch.prmtop -lp bal.prmtop -y *.mdcrdMMPBSA.py.MPI being run on 12 processors
ptraj found! Using /Users/tzotzos/Programs/amber11/AmberTools/bin/ptraj
sander found! Using /Users/tzotzos/Programs/amber11/AmberTools/bin/sander
Preparing trajectories with ptraj...
50 frames were read in and processed by ptraj for use in calculation.
Starting calculations
Starting gb calculation...
calculating ligand contribution...
calculating receptor contribution...
calculating complex contribution...
Starting pb calculation...
calculating ligand contribution...
calculating receptor contribution...
calculating complex contribution...
Calculations complete. Writing output file(s)...
Timing:
Processing Trajectories With Ptraj: 0.012 min.
Total GB Calculation Time (sander): 0.580 min.
Total PB Calculation Time (sander): 2.224 min.
Output File Writing Time: 0.010 min.
Total Time Taken: 2.978 min.
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Received on Tue Aug 09 2011 - 08:30:02 PDT
