No, I'm using the AmberTools 1.4 version
On Sep 28, 2011, at 5:23 PM, Jason Swails wrote:
> What version of MMPBSA.py are you using? Are you using the version from
> AmberTools 1.5?
>
> On Wed, Sep 28, 2011 at 10:43 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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
>>> _______________________________________________
>>> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Sep 28 2011 - 09:00:03 PDT
