Thank you Bill. It works.
Regards
George
On Aug 9, 2011, at 5:12 PM, Bill Miller III wrote:
> 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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>
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Received on Tue Aug 09 2011 - 09:00:03 PDT
