AMBER Archive (2009)

Subject: [AMBER] using sqm from AmberTools 1.3

From: Alan (alanwilter_at_gmail.com)
Date: Wed Dec 23 2009 - 04:35:33 CST

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)
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