Amber 11 and AMBER TOOLS 1.5
Rajesh
On Sat, 17 Sep 2011 16:55:51 -0400
Bill Miller III <brmilleriii.gmail.com> wrote:
> 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
>>
>>
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>>
>>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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Received on Sat Sep 17 2011 - 14:30:02 PDT
