I have attached the output files.
Wat I have found that decomposition values seems reasonable for both
GB and PB. Only the B.E values reported by decompose.out files seems
wrong ....Pls have alook at the files which I attached in the first
mail...
Thanks
Rajesh
On Sun, 18 Sep 2011 05:21:57 -0400
Jason Swails <jason.swails.gmail.com> wrote:
> On Sat, Sep 17, 2011 at 4:43 PM, Rajesh Raju
><rajesh.raju.mail.chem.tamu.edu
>> wrote:
>
>> Dear AMBER Users,
>>
>> I found a very strange error with MMPBSA.py script. I performed a
>>number
>> of MMPBSA binding free energy (B.E) and decomposition calculations
>>with
>> MMPSA.py.
>>
>> The input files :
>> [1] Binding free energy :
>>
>> &general
>> startframe=1, endframe=5000, interval=1,
>> keep_files=0
>> /
>> &gb
>> saltcon=0.1
>> /
>> &pb
>> istrng=0.1
>> /
>>
>>
>> [2] Decomposition
>>
>> &general
>> startframe=1, endframe=5000, interval=1,
>> keep_files=0
>> /
>> &gb
>> saltcon=0.1
>> /
>> &pb
>> istrng=0.1
>> /
>> &decomp
>> idecomp=4, dec_verbose=0, print_res="1-20"
>>
>>
>> When I checked *.out file created by free energy decomposition
>> calculations, the binding free eenrgy values differs. For PB the
>>Binding
>> free energy value is completely wrong...
>>
>> The bining free energy calculations (calculation 1) gives MMGBSA B.E
>>value
>> of -45.8819 and MMPBSA B.E value of -45.2701 kcal mol-1
>>
>
> This difference arises from the fact that a different technique is
>used to
> calculate the surface area for normal calculations (LCPO is used
>here) and
> for decomposition (another method is used). Therefore, the *only*
> differences you should see in the GB side is in the ESURF term.
>
>
>>
>> The same values which I found from the decompose.out file are
>>-47.9146 and
>> 1453.6005 kcal mol-1
>>
>
> I would agree this is wrong. Can you tell based on a quick look if
>the
> values are parsed from the output file correctly? I'm guessing this
>is an
> issue with the decomposition as it's implemented in PBSA, but I
>can't
> comment any further than that. (We need to rule out an MMPBSA.py
>internal
> error, but I don't think there is one). Hopefully one of the PBSA
>folks can
> take a look at this.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Sun Sep 18 2011 - 12:00:03 PDT
