AMBER Archive (2004)

Subject: Re: AMBER: antechamber/Mopac: strange GTP charges

From: David A. Case (case_at_scripps.edu)
Date: Fri May 14 2004 - 14:20:24 CDT

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_at_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
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu