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>_______
> ______________________________
__________
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>
> --
> 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
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Received on Wed May 16 2012 - 18:30:02 PDT
