Bill
Thanks for the prompt reply
Run1: mmpbsa.in
Input file for running PB and GB
&general
endframe=50, verbose=1,
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/
Run 2: mmpbsa.in
Input file for running PB and GB
&general
strip_mdcrd=0
endframe=50, verbose=1,
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/
On Sep 28, 2011, at 3:27 PM, Bill Miller III wrote:
> What does your mmpbsa.in file look like? Are you calculating the binding
> energy for all frames or only a select number of frames? If you are only
> using a select number of frames I would bet that the two methods selected
> different frames to evaluate and that resulted in the discrepancy that you
> are reporting here.
>
> -Bill
>
> On Wed, Sep 28, 2011 at 9:20 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Hi everybody,
>>
>> I'd appreciate any comments / help on the discrepancies shown below.
>>
>> I run MMPBSA.py on the same 20ns trajectory twice.
>>
>> 1. Run 1
>>
>> mpirun -np 12 MMPBSA.py.MPI -O -i mmpbsa.in -o RESULTS.dat -sp
>> complex_solv.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop
>> -y *.mdcrd
>>
>> *.mdcrd represents 10x2ns trajectories
>>
>> 2. Run 2
>>
>> Step 1. merge the 2ns trajectories into a 20ns.mdcrd while stripping waters
>> and ions
>>
>> Step 2. generated new topology files for complex, receptor and ligand
>>
>> run MMPBSA.py
>>
>> mpirun -np 12 MMPBSA.py.MPI -O -i mmpbsa.in -o RESULTS.dat -cp
>> comp_new.prmtop -rp rec_new.prmtop -lp lig_new.prmtop -y *.mdcrd
>>
>> Result of Run1.
>>
>> DELTA G binding = -28.8956 +/- 2.8508
>> 0.1275
>>
>> Result of Run2
>>
>> DELTA G binding = -26.5181 +/- 2.6507
>> 0.3749
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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 Wed Sep 28 2011 - 07:00:04 PDT
