Hi,
MMPBSA is a trajectory post-processing tool, so you dont need to rerun
long MD sims, just use the trajectory files that you have as input. A
typical calculation takes a few hours, instead of days for the MD. Check
the examples in the src/mmpbsa directory, they are fairly detailed. Or
check out the MMPBSA Amber tutorial:
http://ambermd.org/tutorials/advanced/tutorial3/
Regards,
Thomas
On Wed, September 22, 2010 12:30 am, hirdesh kumar wrote:
> Hi Thomas,
> As you have mentioned about the MM-PBSA calculation. So Does it mean that
> the Liu has to run again the simulation including some more parameters for
> MM-PBSA calculations in the starting script or he can do the MM-PBSA
> analysis on the same previous output files. The question may be so weird
> but
> as I am new to this term that's y i m asking.
>
> Hirdesh
>
> On Wed, Sep 22, 2010 at 9:48 AM, <steinbrt.rci.rutgers.edu> wrote:
>
>> Hi,
>>
>> as Bill already wrote, the total potential energy of the protein is not
>> what you want if you are comparing the stability of two solvated
>> conformers. The total free energy change upon changing the conformation
>> is
>> much more useful here. This sounds like a perfect application for
>> MM-PBSA,
>> check out the examples in the MMPBSA directory of amber, one of them
>> does
>> exactly what you probably want.
>>
>> Kind Regards,
>>
>> Thomas
>>
>> On Tue, September 21, 2010 1:42 pm, Bill Ross wrote:
>> >> I have completed two solvent explicit simulations for two possible
>> >> conformations of my protein. In order to know which one is more
>> stable,
>> >> I need to compute the total potential energy form my protein
>> >> without solvent.
>> >
>> > This might tell you which was more stable in vacuum. Is that useful?
>> > E.g. the conformations may not even be attainable in vacuum.
>> >
>> > Bearing in mind that you may be on the wrong track, it is possible
>> > to get the energy of the solute alone by extracting the coordinates
>> > for just those atoms with ptraj, e.g. into pdb, then loadpdb and
>> > saveamberparm to create a prmtop/inpcrd, and run a single-step
>> > energy minimization.
>> >
>> > Bill
>> >
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> Dr. Thomas Steinbrecher
>> BioMaps Institute
>> Rutgers University
>> 610 Taylor Rd.
>> Piscataway, NJ 08854
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Sep 21 2010 - 22:00:05 PDT
