What version of Amber and AmberTools are you using?
-Bill
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
>
> The same values which I found from the decompose.out file are -47.9146 and
> 1453.6005 kcal mol-1
>
> Since I used the same input files and same number of frames I supposed to
> get the same values for GB and PB B.Es. I have also attached the
> outputfiles...
>
> I have seen the same error for the other sets of calculations.
>
> I appreciate ur help..
>
> Thanking u in advance
> Rajesh
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Sep 17 2011 - 14:00:04 PDT
