Hi Dave,
thanks for your mopac 5 experiment!
On Friday 14 May 2004 21:20, David A. Case wrote:
> On Fri, May 14, 2004, Raik Grnberg wrote:
> > thanks for your fast response! I'll wait for the GTP parameters that
> > Heather kindly offered. Nevertheless, in order to learn something here,
> > it would still be nice to know what went wrong. I've put my mopac input
> > and output on the web
> > http://www.raiks.de/archive/mopac7/
>
> Well, it is pretty obvious that your calculation has blown up. Note that
> in the optimized geometry, the first P atom is 50 Angstroms away from all
> of the rest of the atoms!
>
> I would suggest trying the "1SCF" keyword, to see what results you get
> at the starting configuration. I have included below the results I get
> using mopac509mn, which you can compare to mopac7.
It seems, I can not reproduce the Mopac 5 results with Mopac 7.
I first specified "1SCF" as -mk option to antechamber.. but that made the
other key words (AM1, MMOK,..) disappear from the ANTECHAMBER_MUL.MOP file
(antechamber bug or feature?). I instead added the 1SCF key word to the
previous input and run mopac manually. The result is very similar to before
(now the P is 37 A away).
Actually, it's 40A away already in the first coordinate set that mopac prints
(with or without 1SCF). Things seem to go wrong pretty early.
>
> [Geometry optimization of these sorts of complexes with the AM1 Hamiltonian
> can be treacherous. The "divcon" program, from Penn State, optimizes your
> starting geometry by abstracting a proton from the C8 position of the base
> and transferring it to one of the phosphrous oxygens! Of course, this
> might be the "correct" quantum answer: working in the gas phase with a 4-
> ion probably is not at all what you want to do....].
Good point...
Many thanks!
Raik
>
> ...regards...dac
>
>
>
> ***************************************************************************
>**** ** Welcome to MOPAC 5.09 - A version of MOPAC for Direct Molecular
> Dynamics *
> ***************************************************************************
>****
>
> AM1 CALCULATION RESULTS
>
>
>
> ***************************************************************************
>**** * MOPAC: VERSION 5.09 CALC'D. 14-May-04
> * GEO-OK - OVERRIDE INTERATOMIC DISTANCE CHECK
> * MMOK - APPLY MM CORRECTION TO CONH BARRIER
> *
> *
> *
> * CHARGE ON SYSTEM = -4
> *
> *
> *
> * T= - A TIME OF 7200.0 SECONDS REQUESTED
> * DUMP=N - RESTART FILE WRITTEN EVERY 36000.0 SECONDS
> * 1SCF - DO 1 SCF AND THEN STOP
> * AM1 - THE AM1 HAMILTONIAN TO BE USED
>
> ***********************************************************************100B
>Y100 AM1 1SCF MMOK GEO-OK CHARGE=-4
> remark line goes here
>
> ....skipping....
>
>
> 1SCF WAS SPECIFIED, SO BFGS WAS NOT USED
> SCF FIELD WAS ACHIEVED
>
>
> AM1 CALCULATION
> VERSION 5.09
> 14-May-04
>
>
>
>
> FINAL HEAT OF FORMATION = -349.25621 KCAL
>
>
> TOTAL ENERGY = -7342.50619 EV
> ELECTRONIC ENERGY = -52719.20592 EV
> CORE-CORE REPULSION = 45376.69972 EV
>
> IONIZATION POTENTIAL = -5.49361
> NO. OF FILLED LEVELS = 90
> MOLECULAR WEIGHT = 519.151
>
>
> SCF CALCULATIONS = 1
> COMPUTATION TIME = 18.286 SECONDS
>
>
> ...skipping....
>
> EIGENVALUES
>
> -35.18618 -33.89508 -32.74932 -31.23758 -30.25801 -29.65910 -27.86474
> -27.09425 -26.74894 -25.69319 -23.45495 -22.65636 -21.85473 -21.61387
> -21.37740 -21.03164 -20.45091 -19.59101 -19.55670 -18.93994 -18.34104
> -18.15606 -17.56545 -17.10607 -16.96123 -15.63441 -14.10179 -13.83113
> -12.58321 -12.08436 -11.76437 -11.39566 -10.61185 -10.55744 -9.90659
> -9.71045 -9.35233 -9.31149 -8.55527 -8.36710 -8.10966 -7.48803
> -7.40471 -7.26732 -6.78935 -6.62970 -6.44375 -6.27399 -6.15223
> -5.93333 -5.36034 -4.89229 -4.62747 -4.42570 -4.33453 -4.11222
> -4.03031 -3.97427 -3.50664 -3.46894 -3.30888 -3.16371 -2.52880
> -2.43449 -2.30188 -1.98059 -1.59564 -1.26150 -1.09918 -0.95459
> -0.65924 -0.22462 0.35856 0.69227 1.02329 1.15172 1.42865
> 1.77261 1.87312 1.90999 2.79409 2.95293 3.39435 3.45586 3.57320
> 3.77095 3.87385 4.02583 4.10161 5.49361 6.61343 7.93960
> 8.15314 8.87217 9.19616 9.59153 10.10093 10.25102 10.32549
> 10.50684 10.68638 10.90718 10.94947 11.14535 11.35505 11.47793
> 11.58799 11.69007 11.92444 12.13717 12.20077 12.28255 12.43228
> 12.55738 12.66596 12.72576 13.11223 13.18975 13.24654 13.44968
> 13.60931 13.73304 13.90862 14.04424 14.14622 14.21407 14.28517
> 14.77968 15.63667 16.81561 18.34661 18.76014 19.34918 20.46860
> 20.80933 21.76833 22.17104 22.41021 22.74870 23.23165
>
>
> NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS
>
> ATOM NO. TYPE CHARGE ATOM ELECTRON DENSITY
> 1 P 2.6257 2.3743
> 2 O -1.2905 7.2905
> 3 O -1.1960 7.1960
> 4 O -1.1449 7.1449
> 5 P 2.6836 2.3164
> 6 O -1.2308 7.2308
> 7 O -1.2130 7.2130
> 8 O -1.2244 7.2244
> 9 P 2.5997 2.4003
> 10 O -1.1725 7.1725
> 11 O -1.1987 7.1987
> 12 O -1.2105 7.2105
> 13 O -0.7652 6.7652
> 14 C 0.0384 3.9616
> 15 H 0.1015 0.8985
> 16 H 0.1038 0.8962
> 17 C 0.0501 3.9499
> 18 H 0.0936 0.9064
> 19 O -0.2664 6.2664
> 20 C 0.1772 3.8228
> 21 H 0.1260 0.8740
> 22 N -0.1997 5.1997
> 23 C -0.0236 4.0236
> 24 H 0.2600 0.7400
> 25 N -0.0990 5.0990
> 26 C -0.2969 4.2969
> 27 C 0.4078 3.5922
> 28 O -0.4145 6.4145
> 29 N -0.3494 5.3494
> 30 H 0.1928 0.8072
> 31 C 0.1320 3.8680
> 32 N -0.4250 5.4250
> 33 H 0.2089 0.7911
> 34 H 0.2258 0.7742
> 35 N -0.2429 5.2429
> 36 C 0.0305 3.9695
> 37 C 0.0382 3.9618
> 38 H 0.1164 0.8836
> 39 C -0.0563 4.0563
> 40 H 0.1862 0.8138
> 41 O -0.3651 6.3651
> 42 H 0.2070 0.7930
> 43 O -0.4162 6.4162
> 44 H 0.1962 0.8038
> DIPOLE X Y Z TOTAL
> POINT-CHG. -13.461 -37.464 -55.124 67.995
> HYBRID -0.368 -1.343 -2.227 2.626
> SUM -13.829 -38.807 -57.350 70.614
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon May 17 2004 - 16:53:00 PDT
