Hi,
PBTOT and GBTOT are two different results from the Poisson Boltzmann and
Generalized Born solvation models. Neither is right or wrong per se, you
have to look up the theory behind them to judge which would be a good
model in your case. Which one to choose for interpretation is an ongoing
research question in my opinion...
Kind Regards,
Thomas
On Wed, September 22, 2010 9:56 am, Liu, Jingyuan wrote:
> Hi All,
> Thank you so much for your response and input. I actually have run mmpbsa
> for my two complexes as suggested by Thomas. Is the PBTOT or GBTOT that I
> need to look at? Please excuse me for my ignorance. Thanks a lot?
> jingyuan
>
> -----Original Message-----
> From: hirdesh kumar [mailto:hirdeshs8.gmail.com]
> Sent: 2010年9月22日 0:31
> To: AMBER Mailing List
> Subject: Re: [AMBER] How to calculate total potential energy for protein
> chain only?
>
> 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
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> Dr. Thomas Steinbrecher
>> BioMaps Institute
>> Rutgers University
>> 610 Taylor Rd.
>> Piscataway, NJ 08854
>>
>> _______________________________________________
>> AMBER mailing list
>> 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 Thu Sep 23 2010 - 00:00:06 PDT
