Try adding strip_mdcrd=0 to the &general section of the input file to tell MMPBSA.py not to try stripping out the water molecules.
-Bill
On Aug 9, 2011, at 11:01 AM, George Tzotzos <gtzotzos.me.com> wrote:
> 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 - 08:30:03 PDT
