Personally, I would suggest using MMPBSA.py here. You can see all the
details for the QM/MM options on page 200 of the AmberTools 1.5 manual for
MMPBSA.py. The QM/MM options will all go inside the &gb namelist section of
the mmpbsa.in file.
I hope that helps.
-Bill
On Tue, Jun 28, 2011 at 5:27 AM, Aust, Susanne <saust.ipb-halle.de> wrote:
>
> Hello Thomas and all Amber-users,
>
> I extract all snapshots from the trajectory file and now I will try to
> calculate the interaction energy with MM-GBSA over the QM/MM MD results with
> the new Ambertolls 1.5.
> Can I use the mm_pbsa.pl or should I use the mm_pbsa.py?
> Do you have an example of the mmpbsa.in for especially QM/MM results? I
> don't know, how I can say that the results come from QM/MM MD. The user
> manual goes not in so detail at this part.
>
> Thank's a lot!
>
> Susanne
>
>
>
> -----Ursprüngliche Nachricht-----
> Von: steinbrt.rci.rutgers.edu [mailto:steinbrt.rci.rutgers.edu]
> Gesendet: 10 March 2011 12:43
> An: AMBER Mailing List
> Betreff: Re: [AMBER] interaction energy
>
>
> Hi,
>
> > I calculate the average structure over the equilibrated part of the QM/MM
> > MD, so I hope, I have a realistic ensemble.
>
> Id still say that a single structure, average or not, is not a good
> representation of an ensemble. Imagine a symmetric double well potential.
> The average structure would sit on top of the energy barrier and does not
> capture either of the relevant low energy conformations. Add the rugged
> landscape of a protein and minimization may not get you very far from the
> bad average structure. Why not at least minimize 1000 complex structures
> from MD and average the energy if you cant use MMPBSA?
>
> > I try to calculate MM-GBSA and PBSA, but I got positive values for PBtot
> > (for example 60.41 kcal and GBtot 2.02 kcal/mol) When I search for the
>
> Are you sure that the Zn ion is the reason for the problematic results?
> Adjusting the Zn radius or distributing some of the charge to its ligands
> may help, but i agree that this doesnt sound very hopeful. However, the
> approach you suggest amounts to just taking the E(GAS) from MMPBSA and
> hoping it will tell you something about ligand binding, which it may well
> not.
>
> > the failure. Can I use the QM/MM-MD for the MM-GBSA calculations?
>
> AFAIK not without tweaking the scripts.
>
> > I restraint the md simulation relatively restrictive, by reason of time,
> > could there be the failure?
>
> Artificial restraints would tend towards not giving you a good structural
> ensemble, but I doubt the effect is very big if your starting structure is
> reasonable.
>
> > Yes I know, that the Khandelwal et. al (2005)paper is due to methods not
> > the best, but my boss like QM/MM calculation and Khandelwal got an r˛ of
> > 0.9 with this approach. So we try to go this way, but with the Amber
> > forcefield.
>
> On the danger of sounding snarky, 'not the best methods' would tend to
> give 'not the best results', prior publications notwithstanding ;-)
>
> Kind Regards,
>
> Thomas
>
> Fruehlingshaft? Hier eher nicht...
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Jun 28 2011 - 04:00:06 PDT
