Jason
stripping water/ions and merging the trajectory files was done with the following input file
trajin prod_2ns.mdcrd
.................
trajin prod_20ns.mdcrd
strip :WAT
strip :Na+
trajout prod_0-20ns.mdcrd netcdf
As you can see, netcdf is included
I don't see any great discrepancy in the GB results (see below)
Trajectories stripped of water/ions via the above method submitted to MMPBSA.py give
Generalized Born
DELTA G binding = -33.4702 +/- 1.8177 0.2571
Poisson Boltzmann
DELTA G binding = -26.5181 +/- 2.6507 0.3749
Trajectories NOT stripped of water/ions PRIOR to being submitted to MMPBSA.py
Generalized Born
DELTA G binding = -34.3190 +/- 2.0987 0.0939
Poisson Boltzmann
DELTA G binding = -28.8956 +/- 2.8508 0.1275
I've tried to re-run MMPBSA.py including netcdf=1 as per your suggestion
Input file for running PB and GB
&general
strip_mdcrd=0
endframe=50, verbose=1,
netcdf=1,
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/
I get "Warning: Input error! "netcdf=1" is an invalid option."
I also tried it at &gb and &pb. MMPBSA.py issues the same error message as above.
On Sep 28, 2011, at 4:16 PM, Jason Swails wrote:
> When you stripped all waters and everything else, did you do anything else?
> (For instance, did you align via RMSD, etc.)?
>
> Here is my suggestion. Work *completely* in NetCDF trajectories. I don't
> know if your initial trajectories are NetCDF (I would strongly encourage you
> to use NetCDF if you're not). Make sure the stripped trajectory that you
> make is created as a NetCDF trajectory. Then, use netcdf=1 in your
> MMPBSA.py input file. This will force MMPBSA.py to use NetCDF for the
> temporary internal files.
>
> I'd be curious to see if the (vastly) increased precision of a NetCDF
> trajectory can account for some of this difference...
>
> Also, you never say whether the discrepancy arises in the PB results or GB
> results (I would expect the PB results, yes?).
>
> All the best,
> Jason
>
> On Wed, Sep 28, 2011 at 9:33 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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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>>>> 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
>>
>>
>> _______________________________________________
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>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Sep 28 2011 - 08:00:03 PDT
