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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Received on Sat Sep 17 2011 - 14:00:02 PDT
