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AMBER Archive (2009)Subject: Re: [AMBER] using sqm from AmberTools 1.3
From: Alan (alanwilter_at_gmail.com)
Hi there,
Now that I am looking deeper at this problematic molecule, I am getting even
First, the molecule is the ligand GNP in 1E0A from PDB:
Looking only at the ligand:
The problem is that in the complex 1E0A (done in pH 5.5), GNP has only 13 H
So, GNP from the PDB 1E0A has 45 atoms (lets called it GNP_1E0A) and GNP
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
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
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,
- mopac.pdb generated at the end of calculation of GNP_1E0AM0 has
- Atom types identification and hence topology parameters were equal
- It seems that GNP_1E0A is a bad structure (but it was the one obtained by
So in the end I am trying to find a way of improving the structure of the
I still have to try GNP_1E0A with a more relaxed criteria for sqm (but first
If you're brave enough to get reading till hear and happen to have any
Cheers,
Alan
On Thu, Dec 24, 2009 at 23:17, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Hi 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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