AMBER Archive (2009)

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

From: Alan (alanwilter_at_gmail.com)
Date: Tue Dec 29 2009 - 11:35:06 CST

Hi there,

Now that I am looking deeper at this problematic molecule, I am getting even
more puzzled.

First, the molecule is the ligand GNP in 1E0A from PDB:
http://www.pdb.org/pdb/explore/explore.do?structureId=1E0A

Looking only at the ligand:
http://www.pdb.org/pdb/ligand/ligandsummary.do?hetId=GNP&sid=1E0A
 and
http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?FUNCTION=record&ENTITY=CHEM_COMP&PRIMARYKEY=GNP&PARENTINDEX=-1&APPLICATION=1

The problem is that in the complex 1E0A (done in pH 5.5), GNP has only 13 H
and not 17 H as shown in formula or in the ligand links above.

So, GNP from the PDB 1E0A has 45 atoms (lets called it GNP_1E0A) and GNP
alone has 49 atoms.

So I ran antechamber for 4 cases:

GNP_1E0AM0 = GNP_1E0A with net charge 0 and with mopac

GNP_1E0AS0 = same as above but "tried" to calculate with sqm (failed)

GNP45M0ideal = GNP49 "ideal" structure from
ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/pdb/GNP.pdb generated
by Corina and modified to have 45 atoms (removed 4 extra H), calculated with
net charge 0 and mopac

GNP45S0ideal = same as above but this time calculated with sqm

Please, see the PDF in attach which contains a table and a graphic.

So, trying to summarise. GNP_1E0AS0 failed, even after 10 hours. From
sqm.out log file, some excerpts:

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 = -0.1214E+07 DeltaE = -0.6864E+03 DeltaP = 0.9693E+00

QMMM: Smallest DeltaE = 0.1329E+00 DeltaP = 0.7212E+00 Step = 178

sqm energy: 10 -209.6926 14.675553

sqm energy: 20 -211.5094 10.486989

sqm energy: 30 -268.9268 13.880247

sqm energy: 40 -401.5650 42.071925

sqm energy: 50 -366.5877 37.926958

sqm energy: 60 -429.6233 14.323823

sqm energy: 70 -400.2295 14.318731

sqm energy: 80 -367.3231 34.942109

sqm energy: 90 -381.7879 14.257946

sqm energy: 100 -371.7226 24.295281

sqm energy: 110 -467.3020 19.901647

sqm energy: 120 -425.3893 17.823669

sqm energy: 130 -455.1285 24.254097

sqm energy: 140 -507.5694 25.748950

sqm energy: 150 -433.3815 24.008427

sqm energy: 160 -429.6812 12.218396

sqm energy: 170 -383.5559 18.717593

sqm energy: 180 -397.6311 17.364066

sqm energy: 190 -388.3367 11.428950

sqm energy: 200 -348.8810 36.352170

sqm energy: 210 -402.6649 9.153514

sqm energy: 220 -294.3676 15.545350

sqm energy: 230 -385.1098 5.674296

sqm energy: 240 32.6554 210.573321

sqm energy: 250 -439.3152 22.846344

sqm energy: 260 -381.9286 34.739349

sqm energy: 270 -463.9568 6.414177

sqm energy: 280 -379.2817 12.407676

sqm energy: 290 -415.8038 22.961298

sqm energy: 300 -346.6908 35.655386

sqm energy: 310 -387.7468 20.213585

sqm energy: 320 -325.3272 10.360355

sqm energy: 330 -327.5408 12.264327

sqm energy: 340 -340.5160 6.890082

sqm energy: 350 -394.5466 8.379747

sqm energy: 360 -332.0989 6.348266

sqm energy: 370 -331.4230 9.617969

sqm energy: 380 -305.3395 15.270744

sqm energy: 390 -332.4898 12.597410

sqm energy: 400 -366.1705 6.273944

sqm energy: 410 -315.7876 21.826861

sqm energy: 420 -338.1509 14.780086

sqm energy: 430 -356.9402 15.870415

sqm energy: 440 -386.9407 11.709662

sqm energy: 450 -331.0573 8.897118

sqm energy: 460 -1020.1813 95.297319

sqm energy: 470 -1020.1813 95.297319

sqm energy: 480 -1020.1813 95.297319

sqm energy: 490 -1020.1813 95.297319

sqm energy: 500 -1020.1813 95.297319

sqm energy: 510 -1020.1813 95.297319

sqm energy: 520 -1020.1813 95.297319

sqm energy: 530 -1020.1813 95.297319

sqm energy: 540 -1020.1813 95.297319

sqm energy: 550 -1020.1813 95.297319

sqm energy: 560 -1020.1813 95.297319

sqm energy: 570 -1020.1813 95.297319

sqm energy: 580 -1020.1813 95.297319

sqm energy: 590 -1020.1813 95.297319

sqm energy: 600 -1020.1813 95.297319

Some notes:

- For the other 3 situations that I was able to obtain the am1-bcc charges,
I guess they are fine (please, see graphic), with GNP_1E0AM0 showing more
deviation.

- mopac.pdb generated at the end of calculation of GNP_1E0AM0 has
structure/conformation totally rubbish (ask in private if you want to see it
or try to reproduce it).

- Atom types identification and hence topology parameters were equal
for GNP45M0ideal and GNP45S0ideal, and both differed slightly
from GNP_1E0AM0 (if you want this data, please request in private).

- It seems that GNP_1E0A is a bad structure (but it was the one obtained by
NMR for 1E0A anyway, in pH 5.5) and it seems that Corina improves this
structure (although in the ligands DB it's with 49 atoms, would it be its
original case when in pH 7?)

So in the end I am trying to find a way of improving the structure of the
ligand in a way that antechamber (with sqm) can carry out. Corina is not
free. Is there a way of trying to obtaining this with GNU or free software?

I still have to try GNP_1E0A with a more relaxed criteria for sqm (but first
attempts toward that were deceptive, but I may need to wait longer...)

If you're brave enough to get reading till hear and happen to have any
suggestion to share, I would really appreciate and be thankful.

Cheers,

Alan

On Thu, Dec 24, 2009 at 23:17, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
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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