I'm doing so right now. Will report accordingly
Thanks
George
On Sep 28, 2011, at 6:03 PM, Bill Miller III wrote:
> Try upgrading to AmberTools 1.5 and see if you get the same issues.
>
> -Bill
>
> On Wed, Sep 28, 2011 at 11:44 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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
>>>>>>>> _______________________________________________
>>>>>>>> AMBER mailing list
>>>>>>>> AMBER.ambermd.org
>>>>>>>> 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
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>> --
>>> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 28 2011 - 09:30:04 PDT
