Gabriel,
If the method does not converge, then it may simply not be suitable for the
system you want to model. However, there are a lot of things that probably
need to be additionally considered:
1.) The default AM1/d model (AM1/d-PhoT) was not designed for
polyphosphates or nucleobases, as such ATP could be problematic on its
own. Does it optimize sensibly in the gas phase?
2.) The QM region you describe is quite large, does a smaller system
converge SCF? The Lysine sidechain in particular bothers me since
AM1/d-PhoT was not parameterized with nitrogen in mind *at all*.
3.) The (default) Mg parameters from Imhof, et al. have NOT been
extensively validated with AM1/d-PhoT.
4.) Perhaps trivial, but have you double checked your charge and link atom
selections? This probably isn't an issue since other methods converge, but
is usually my first goto when things go badly wrong.
5.) Also possibly trivial, but have you spent a lot of time optimizing the
MM region? Putting sensible charges (gas phase mulliken perhaps?) and
Lennard-Jones parameters on your QM region and then optimizing should help
immensely if you haven't done that already.
6.) Probably not relevant until you do dynamics, but be sure to use the
QM/MM switching function, as energy is otherwise not well conserved,
especially with d-orbitals. This is not the default (for backwards
compatibility only).
Brian
On Wed, May 16, 2012 at 9:02 PM, Gabriel Jara
<gabriel.fcq.unc.ar.gmail.com>wrote:
> H Andreas
>
> Sorry for my delayed answer. The main problema is that the Qm region of my
> system does not converge using AM1D formalism, but it work pretty well when
> i use AM1, PM3, PM6 or DFTB. Because there are many publications using
> AM1D for studying ATP hydrolysis in kinases, we are interest of using AM1D.
>
> Thanks in advances.
>
> Gabriel
>
>
> Message: 10
> Date: Sat, 12 May 2012 03:15:37 -0700
> From: Andreas Goetz <agoetz.sdsc.edu>
> Subject: Re: [AMBER] am1d problem
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <2AB5BFE1-2B8A-40F0-B1D5-E140749A01DB.sdsc.edu>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi Gabriel,
>
> PM6 is not the solution to everything. It may well be that bond distances
> predicted by other Hamiltonians are in better agreement with experiment. If
> you send me your input files I can double check against other PM6
> implementations.
>
> All the best,
> Andy
>
> On May 11, 2012, at 5:36 PM, Gabriel Jara wrote:
>
> > Hi Andreas,
> >
> > Thanks for your answer. I tried with AM1, PM3 and PM6. With these methods
> I
> > found SCF convergence and a reasonable molecular geometry. However, with
> > PM6, i found the P-O of the ATP in the kinase protein quite long 1.8 to 2
> > ?. A collegue run another kinase protein (fron other family) with a mdin
> > file similar, and He found the same difficulties I found.
> >
> > Thanks in advance
> >
> > Gabriel Jara
> >
> >
> >
> > Message: 10
> > Date: Mon, 7 May 2012 13:40:35 -0700
> > From: Andreas Goetz <agoetz.sdsc.edu>
> > Subject: Re: [AMBER] am1d problem
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID: <BED4FAFD-1691-4008-9CDC-5734BED5B683.sdsc.edu>
> > Content-Type: text/plain; charset=iso-8859-1
> >
> > Hi Gabriel,
> >
> > If your SCF does not converge, the forces will be meaningless and
> > consequently the optimized geometry and/or MD trajectory. Since you say
> > that DFTB does not suffer from this problem it might be specific to the
> > AM1D implementation. Did you try other NDDO type Hamiltonians that
> support
> > the elements of your QM region? Does the SCF converge with AM1/PM3/PM6
> and
> > do you get a reasonable geometry?
> >
> > All the best,
> > Andy
> >
> >
> > On May 3, 2012, at 3:10 PM, Gabriel Jara wrote:
> >
> >> Hi,
> >>
> >> I am running qmmm calculations using AM1D. The system of interest is a
> >> kinase with one atp molecule and two magnesium cations within a protein
> >> environment. The QM region includes the atp molecule, magnesium cations
> > and
> >> side chain of a threonine, a aspartic and a lysine.
> >>
> >> Both in optimization and MD each atom of the QM region starts to move
> away
> >> from each other. When I did this same thing using DFTB that problem did
> > not
> >> happen.
> >>
> >> Also, the mdout show the next message in both optimization and MD.
> >>
> >> QMMM: WARNING!
> >> QMMM: Unable to achieve self consistency to the tolerances specified
> >> QMMM: No convergence in SCF after 2000 steps.
> >> QMMM: Job will continue with unconverged SCF. Warning energies
> >> QMMM: and forces for this step will not be accurate.
> >> QMMM: E = -0.8693E+06 DeltaE = -0.5769E+03 DeltaP = 0.1544E+01
> >> QMMM: Smallest DeltaE = 0.3633E-01 DeltaP = 0.1045E+01 Step = 210
> >>
> >> In the optimization this message is not showed if i use the keywords
> >> ndiis_attempts=50 ndiis_matrices=10. However the QM structure continue
> >> destroying itself in the optimization.
> >>
> >> I attach the mdin file for the optimization.
> >>
> >> Thanks in advance.
> >>
> >> Gabriel
> >>
> >>
> >> --
> >> Dr. Gabriel E. Jara
> >> INQUIMAE - CONICET
> >> Facultad de Ciencias Exactas y Naturales
> >> Universidad de Buenos Aires
> >>
> >>
> >>
> >>
> >> --
> >> Dr. Gabriel E. Jara
> >> INFIQC - CONICET
> >> Departamento de Qu?mica Org?nica
> >> Facultad de Ciencias Qu?micas
> >> Universidad Nacional de C?rdoba
> >> Tel: ++54-351-4334170/4173 int. 132
> >> Fax: ++54-351-4333030
> >> X5000HUA - C?rdoba -Argentina
> >> <AM1_term-from-dftb.in>_______
> > ______________________________
> __________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > --
> > Dr. Andreas W. Goetz
> > Assistant Project Scientist
> > San Diego Supercomputer Center
> > Tel : +1-858-822-4771
> > Email: agoetz.sdsc.edu
> > Web : www.awgoetz.de
> >
> >
> > --
> > Dr. Gabriel E. Jara
> > INQUIMAE - CONICET
> > Facultad de Ciencias Exactas y Naturales
> > Universidad de Buenos Aires
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel : +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web : www.awgoetz.de
>
>
> Dr. Gabriel E. Jara
> INQUIMAE - CONICET
> Facultad de Ciencias Exactas y Naturales
> Universidad de Buenos Aires
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
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Received on Wed May 30 2012 - 19:30:03 PDT
