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 - 02:30:02 PDT
