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 - 06:30:04 PDT
