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.
[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....].
....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
***********************************************************************100BY100
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
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
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Received on Fri May 14 2004 - 20:53:00 PDT
