AMBER Archive (2009)

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

From: David Watson (dewatson_at_olemiss.edu)
Date: Tue Dec 29 2009 - 13:34:28 CST

On Dec 29, 2009, at 11:35 AM, Alan wrote:

> 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
>

1) downloaded 1EOA

> Looking only at the ligand:
> http://www.pdb.org/pdb/ligand/ligandsummary.do?hetId=GNP&sid=1E0A
> and

2) loaded 1EOA into pymol
   sele GNP, resn GNP # to select the GNP molecule
   h_add GNP # to add hydrogens

3) extracted the GNP selection as an object

4) saved this to file as a GNP.pdb

5) opened GNP.pdb in Avogadro

6) withing Avogadro:
   Build -> Add Hydrogens # Note - you may or may not want to do this, as it will affect the charge.
   AutoOptimization Settings -> Force Field -> MMFF94s
   Algorithm: Conjugate Gradient # run this for several seconds
   Algorithm: Steepest Descent # run this for several seconds

7) Save As -> MDL SD file (*mol)

8) Run antechamber:
   antechamber -i GNP.mol -fi mdl -o GNP.mol2 -fo mol2 -s 2 -c bcc -pf y
   # only takes a minute or so on my MacBook 2GHz Core 2 Duo

9) Inspect output (I'll leave this up to you)

> 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
>>
>>
>> _______________________________________________
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>>
>
>
>
> --
> 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)
> <GNP_Mopac_X_Sqm.pdf>_______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber




  • application/octet-stream attachment: sqm.out

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