AMBER Archive (2009)

Subject: RE: [AMBER] using sqm from AmberTools 1.3

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Dec 24 2009 - 17:17:47 CST

Hi Alan,

An energy of 10^7 Kcal/mol looks VERY high to me. I suspect you initial structure is very bad and this is the source of your problems, both in mopac and SQM. I suggest checking your initial structure carefully. You likely have two atoms on top of each other or very close.

Also note the minimizer finds a local minimum, not the global minimum (it would be nice if it did ;-) ). Hence you have to provide a reasonable input structure to obtain a suitable minimum for the AM1-BCC charges.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Alan
> Sent: Wednesday, December 23, 2009 2:36 AM
> To: AMBER Mailing List
> Subject: [AMBER] using sqm from AmberTools 1.3
>
> Hi List,
>
> I am aware about what Prof. Case said in "See note 6 on p. 82 of the
> Users'
> Manual for a discussion".
>
> So I am testing antechamber with sqm.
>
> I have a particular example that only worked fine so far with AT 1.2
> and
> mopac in my laptop (MBP with intel and 64bits). Testing on Linux 64
> bits and
> mopac failed.
>
> Now I am testing this example with AT 1.3 and sqm. It's taking more
> than an
> hour now (not finished) and printing in sqm.out:
>
> -----------------------------------------------------------------------
> ---------
> 4. RESULTS
> -----------------------------------------------------------------------
> ---------
>
>
> QMMM: WARNING!
> QMMM: Unable to achieve self consistency to the tolerances specified
> QMMM: No convergence in SCF after 1000 steps.
> QMMM: Job will continue with unconverged SCF. Warning energies
> QMMM: and forces for this step will not be accurate.
> QMMM: E = -0.1216E+07 DeltaE = -0.8180E+02 DeltaP = 0.2721E+00
> QMMM: Smallest DeltaE = -0.2763E-02 DeltaP = 0.1572E-01 Step =
> 730
>
>
> QMMM: WARNING!
> QMMM: Unable to achieve self consistency to the tolerances specified
> [snip]
>
> QMMM: WARNING!
> QMMM: Unable to achieve self consistency to the tolerances specified
> QMMM: No convergence in SCF after 1000 steps.
> QMMM: Job will continue with unconverged SCF. Warning energies
> QMMM: and forces for this step will not be accurate.
> QMMM: E = -0.1210E+07 DeltaE = -0.3606E+03 DeltaP = 0.4866E+00
> QMMM: Smallest DeltaE = 0.2421E+01 DeltaP = 0.4358E+00 Step =
> 29
> [lastest so far]
>
> First, I note that E = -0.1210E+07 doesn't change, but I am afraid
> that
> with standard criteria for convergence given by sqm "qm_theory=’AM1’,
> grms_tol=0.0002, tight_p_conv=1, scfconv=1" it will never converge
> anyway.
>
> So, what I am trying to figure out is if I see for others cases things
> similar to that above, is it safe to kill the process and try to
> restart
> with a looser criteria as scfconv to 1.d-8 and/or tight_p_conv to 0?
>
> And, would anyone know a program for Mac that would allow me to 'see'
> (liking plotting the E or visualise structures) the sqm.out like
> Avogadro.app does for Gamess out files for example?
>
> Many thanks in advance,
>
> Alan
>
> --
> Alan Wilter Sousa da Silva, D.Sc.
> PDBe group, PiMS project http://www.pims-lims.org/
> EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD,
> UK
> +44 (0)1223 492 583 (office)
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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