Decomposition analysis is only available with amber 11 using MMPBSA.py. There is a bug in the amber 10 code that makes the decomposition results incorrect using MMPBSA.py.
I hope that helps.
-Bill
On Jun 6, 2011, at 11:28 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
> Hi,
> I am using Amber 10. Can I use the AmberTool1.5 with Amber10 or it is only
> compatible with Amber11.
>
> Hirdesh
>
> On Mon, Jun 6, 2011 at 10:44 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
>
>> Yes, AmberTools 1.5 is the latest version of MMPBSA.py and supports energy
>> decomposition analysis.
>>
>> -Bill
>>
>> On Mon, Jun 6, 2011 at 1:12 PM, victor ma <victordsma.gmail.com> wrote:
>>
>>> I'm using AMBER11 with AMBERTOOLS1.4. So i guess I need 1.5 for energy
>>> decomposition?
>>> Thanks.
>>>
>>>
>>>
>>> On Mon, Jun 6, 2011 at 12:10 PM, Bill Miller III <brmilleriii.gmail.com
>>>> wrote:
>>>
>>>> What version of MMPBSA.py are you using? If you download the newly
>>> released
>>>> AmberTools 1.5 from the Amber website, then that version will support
>>>> decomposition analysis.
>>>>
>>>> -Bill
>>>>
>>>> On Mon, Jun 6, 2011 at 1:07 PM, victor ma <victordsma.gmail.com>
>> wrote:
>>>>
>>>>> hi all
>>>>>
>>>>> I'm working on a protein-ligand binding problem and trying to get a
>>>>> per-residue energy decomposition. I followed the tutorial on AMBER's
>>>>> website, add this section into the mmpbsa.infile:
>>>>>
>>>>> &decomp
>>>>> idecomp=3,
>>>>> dec_verbose=1,
>>>>> /
>>>>>
>>>>>
>>>>> However, the run failed and it complains that it couldn't find any
>>>> namelist
>>>>> called "decomp". I checked amber11 manual. It says: "idecomp
>> Specifies
>>>>> whether or not to perform a decomposition analysis. (This option is
>> not
>>>>> currently supported, but will be included in a later version)". It
>> so,
>>>> how
>>>>> do I get decomposed energies out of mmpbsa.py?
>>>>>
>>>>> THanks a lot.
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Best regards,
>>>>>
>>>>> Victor
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>
>>>
>>>
>>> --
>>> Best regards,
>>>
>>> Victor
>>> _______________________________________________
>>> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 06 2011 - 21:00:03 PDT
