Hello,
You should keep these responses on the amber list so it gets archived and
everyone can benefit from them.
Also, the newly released AmberTools 1.5 supplies a significantly upgraded
MMPBSA.py release, so at some point I suggest downloading that and
upgrading.
My responses to your questions are below
On Mon, Apr 18, 2011 at 12:17 PM, vani panguluri <vanipanguluri.gmail.com>wrote:
> I am not able to understand clearly what you are saying below could you
> please explain this clearly........
> where can I find the complex/ligand/receptor topology files for serial
> version.
>
You provided the topology files. You had to create the topology files
before running MMPBSA.py. To test that you made them correctly, you should
try visualizing the created coordinate files (_MMPBSA_complex.mdcrd,
_MMBPSA_receptor.mdcrd, and _MMPBSA_ligand.mdcrd, or .nc if you used
netcdf=1). If the structures look warped, that means that your prmtop files
have problems that you have to fix.
Note that AmberTools 1.5 ships with a utility that will build
complex/receptor/ligand prmtop files from a solvated complex (or unsolvated
complex) topology file called "ante-MMPBSA.py" from a given receptor mask in
amber-mask format. You may be able to use this to help create compatible
topology files.
Good luck,
Jason
>
> regards,
> Vani
>
> On Sun, Apr 10, 2011 at 10:26 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>>
>>
>> On Sun, Apr 10, 2011 at 6:16 PM, vani panguluri <vanipanguluri.gmail.com>wrote:
>>
>>> Hello,
>>>
>>> using the serial version of MMPBSA.py i got the following error.
>>>
>>> ptraj found! Using
>>> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
>>> sander found! Using
>>> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
>>> ptraj found! Using
>>> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
>>> sander found! Using
>>> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
>>> ptraj found! Using
>>> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
>>> sander found! Using
>>> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
>>>
>>
>> This tells me that you're still using MPI commands to launch the serial
>> version of MMPBSA, so it's launching several MMPBSA.py serial jobs all at
>> the same time. This will cause massive problems, as each thread tries to
>> write to exactly the same files, and they will be fighting each other.
>>
>> Review running programs in both serial and parallel to make sure that
>> you're doing it properly.
>>
>>
>>> Calculations complete. Writing output file(s)...
>>>
>>> Error: Sander output is missing values!
>>> VDWAALS = ************* EEL = -5060.4993 EGB =
>>> -14223.5294NOTE: All files have been retained for
>>>
>>
>> This tells me that your files are incompatible (your prmtop files and
>> trajectory files). Make sure that you set up your calculation properly so
>> that the complex/receptor/ligand topology files match the generated
>> trajectory files (you can check this with visualization programs).
>>
>> Good luck,
>> Jason
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>>
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 18 2011 - 12:30:03 PDT
