I would like to recommend to optimize the input structure with other
programs, such as sybyl and/or apply another conformation. The input
structure should be quite "reasonable". The neat thing for AM1 charges lie
that they are not or slightly conformation-dependent.
Best
Junmei
===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang.tbc.com
Homepage: Http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================
Carsten Detering
<detering.u.washi
ngton.edu> To
Sent by: amber.scripps.edu
owner-amber.scrip cc
ps.edu
Subject
AMBER: antechamber + FAILED TO
02/09/2004 01:17 ACHIEVE SCF
PM
Please respond to
amber.scripps.edu
Hi all,
I was able to eliminate one error in the antechamber test (maximum
number of atomic orbitals exceeded - thanks to david case), but the
problem with the unability to achieve self-consistence persists, even
with the parameters MAXHEV and MAXLIT changed. This is the output of the
antechamber/guanine/Run.guanine ANTECHAMBER_MUL.out:
*******************************************************************************
** Welcome to MOPAC 5.010 - A version of MOPAC for Direct Molecular
Dynamics
*******************************************************************************
AM1 CALCULATION RESULTS
*******************************************************************************
* MOPAC: VERSION 5.010 CALC'D. 9-Feb-04
* GEO-OK - OVERRIDE INTERATOMIC DISTANCE CHECK
* MMOK - APPLY MM CORRECTION TO CONH BARRIER
*
*
*
* CHARGE ON SYSTEM = 0
*
*
*
* T= - A TIME OF 3600.0 SECONDS REQUESTED
* DUMP=N - RESTART FILE WRITTEN EVERY 36000.0 SECONDS
* AM1 - THE AM1 HAMILTONIAN TO BE USED
***********************************************************************030BY040
AM1 MMOK GEO-OK CHARGE=0
remark line goes here
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA
NB NC
1 H
2 O 0.96032 * 1
3 C 1.44032 * 118.99517 * 2 1
4 H 1.08921 * 109.48185 * 60.02738 * 3
2 1
5 H 1.09007 * 109.46676 * 300.01505 * 3
2 1
6 C 1.52006 * 109.96697 * 179.99746 * 3
2 1
7 H 1.09024 * 109.46729 * 159.98837 * 6
3 2
8 O 1.45974 * 108.87734 * 273.67410 * 6
3 2
9 C 1.41993 * 110.01449 * 105.61440 * 8
6 3
10 H 1.09038 * 109.47782 * 120.00972 * 9
8 6
11 N 1.49002 * 108.08266 * 232.31432 * 9
8 6
12 C 1.37951 * 129.20706 * 81.56917 * 11
9 8
13 H 1.08020 * 119.98969 * 0.05934 * 12
11 9
14 N 1.31023 * 114.01722 * 180.10676 * 12
11 9
15 C 1.39000 * 103.89517 * 0.03500 * 14
12 11
16 C 1.41970 * 130.42911 * 179.95287 * 15
14 12
17 O 1.23061 * 128.78274 * 0.02933 * 16
15 14
18 N 1.39963 * 111.40637 * 180.01674 * 16
15 14
19 H 1.00058 * 117.36132 * 179.93119 * 18
16 15
20 C 1.37965 * 125.22566 * 359.89403 * 18
16 15
21 N 1.34069 * 116.03640 * 180.02315 * 20
18 16
22 H 1.01013 * 126.95708 * 359.19584 * 21
20 18
23 H 1.00985 * 116.55792 * 180.56205 * 21
20 18
24 N 1.33016 * 123.34585 * 0.00000 * 20
18 16
25 C 1.36034 * 112.16012 * 0.00000 * 24
20 18
26 C 1.53025 * 115.77720 * 30.92548 * 6
3 2
27 H 1.09008 * 109.50780 * 29.97582 * 26
6 3
28 C 1.52980 * 102.78256 * 273.65347 * 26
6 3
29 H 1.08993 * 109.50530 * 120.02606 * 28
26 6
30 H 1.08976 * 109.51551 * 240.04175 * 28
26 6
31 O 1.42016 * 116.50297 * 156.53433 * 26
6 3
32 H 0.96021 * 114.95463 * 180.01649 * 31
26 6
CARTESIAN COORDINATES
NO. ATOM X Y Z
1 H 0.0000 0.0000 0.0000
2 O 0.9603 0.0000 0.0000
3 C 1.6585 1.2598 0.0000
4 H 1.3859 1.8262 0.8895
5 H 1.3849 1.8267 -0.8899
6 C 3.1597 1.0213 0.0001
7 H 3.6701 1.9181 -0.3517
8 O 3.6122 0.8598 1.3785
9 C 3.8984 -0.5064 1.6391
10 H 4.9450 -0.6101 1.9268
11 N 3.1541 -0.9090 2.8655
12 C 1.8340 -1.2864 3.0000
13 H 1.1904 -1.3175 2.1330
14 N 1.4859 -1.5804 4.2284
15 C 2.6508 -1.3853 4.9612
16 C 2.9023 -1.5427 6.3496
17 O 2.1276 -1.8959 7.2381
18 N 4.2307 -1.2357 6.6661
19 H 4.5053 -1.3160 7.6249
20 C 5.1913 -0.8321 5.7618
21 N 6.4085 -0.5858 6.2670
22 H 6.6895 -0.6538 7.2349
23 H 7.1156 -0.2814 5.6134
24 N 4.9558 -0.6871 4.4608
25 C 3.6680 -0.9818 4.1365
26 C 3.6315 -0.2506 -0.7081
27 H 2.9414 -0.4948 -1.5159
28 C 3.5256 -1.3092 0.3913
29 H 2.8341 -2.0913 0.0780
30 H 4.5078 -1.7448 0.5730
31 O 4.9727 -0.2557 -1.1749
32 H 5.2451 -1.0640 -1.6157
H: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985)
C: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985)
N: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985)
O: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985)
RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 51
INTERATOMIC DISTANCES
0
H 1 O 2 C 3 H 4 H 5
C 6
------------------------------------------------------------------------------
H 1 0.000000
O 2 0.960315 0.000000
C 3 2.082710 1.440325 0.000000
H 4 2.459042 2.075412 1.089208 0.000000
H 5 2.459056 2.075875 1.090069 1.779449 0.000000
C 6 3.320662 2.424944 1.520056 2.141388 2.142618
0.000000
H 7 4.156051 3.338563 2.145642 2.601325 2.349525
1.090236
O 8 3.960742 3.109977 2.424301 2.475806 3.322883
1.459743
C 9 4.259185 3.402275 3.289872 3.509349 4.261122
2.359206
H 10 5.342088 4.467947 4.243855 4.436107 5.152327
3.092076
N 11 4.357278 3.721588 3.892525 3.809525 4.971696
3.454972
C 12 3.744086 3.379035 3.938715 3.787185 5.002436
4.010230
H 13 2.775354 2.517632 3.378059 3.386335 4.366035
3.727933
N 14 4.752350 4.544576 5.096638 4.771042 6.149468
5.239182
C 15 5.793084 5.421330 5.709232 5.337874 6.793832
5.537511
C 16 7.149862 6.816778 7.051109 6.592501 8.128100
6.852480
O 17 7.778924 7.572812 7.910054 7.396551 8.970784
7.871760
N 18 7.991399 7.527225 7.568387 7.129998 8.635419
7.118770
H 19 8.953694 8.511041 8.536861 8.060355 9.597697
8.087731
C 20 7.800087 7.196729 7.075027 6.729615 8.112001
6.384409
N 21 8.982671 8.324790 8.077440 7.743555 9.070804
7.239652
H 22 9.875274 9.251767 9.017592 8.633819 10.015234
8.222433
H 23 9.067547 8.335242 7.979033 7.719205 8.920633
6.989637
N 24 6.703019 6.027803 5.878854 5.640440 6.906547
5.103153
C 25 5.615025 5.040421 5.115990 4.861663 6.193967
4.623914
C 26 3.708335 2.774751 2.583666 3.450810 3.065210
1.530252
H 27 3.345857 2.543134 2.649963 3.686804 2.864266
2.155001
C 28 3.781111 2.906485 3.199803 3.828466 4.007236
2.391203
H 29 3.523060 2.809060 3.552186 4.254736 4.288139
3.130511
H 30 4.867556 3.994677 4.180255 4.753799 4.964736
3.129968
O 31 5.116004 4.188673 3.828977 4.632640 4.158129
2.509595
H 32 5.590559 4.701337 4.568909 5.433577 4.876977
3.362791
1
0
H 7 O 8 C 9 H 10 N 11
C 12
------------------------------------------------------------------------------
H 7 0.000000
O 8 2.029030 0.000000
C 9 3.145420 1.419926 0.000000
H 10 3.634391 2.058546 1.090375 0.000000
N 11 4.313866 2.355787 1.490018 2.044017 0.000000
C 12 4.987341 3.224436 2.592653 3.359653 1.379508
0.000000
H 13 4.774106 3.342901 2.869687 3.826235 2.135315
1.080205
N 14 6.163414 4.312493 3.698374 4.266665 2.256337
1.310227
C 15 6.338709 4.336018 3.655891 3.882327 2.207311
2.126854
C 16 7.581151 5.566654 4.924898 4.960217 3.550161
3.525185
O 17 8.633165 6.643285 6.034503 6.148293 4.598611
4.291822
N 18 7.714290 5.721229 5.090467 4.833531 3.963600
4.380301
H 19 8.647714 6.674524 6.070691 5.758502 4.964171
5.341029
C 20 6.874106 4.956822 4.332976 3.849399 3.541884
4.371025
N 21 7.587904 5.814400 5.265428 4.580449 4.718698
5.664860
H 22 8.560849 6.786647 6.255000 5.587647 5.626355
6.473843
H 23 7.231262 5.613394 5.118149 4.290743 4.861861
5.977818
N 24 5.621365 3.701140 3.018681 2.535202 2.416646
3.498361
C 25 5.343538 3.316798 2.552616 2.579097 1.372829
2.178933
C 26 2.198160 2.363676 2.376123 2.965968 3.664959
4.248884
H 27 2.776382 3.265254 3.296943 3.984880 4.406065
4.716532
C 28 3.314866 2.384620 1.529913 2.204812 2.533799
3.109210
H 29 4.118122 3.317449 2.466130 3.172955 3.044774
3.191575
H 30 3.869588 2.869598 1.744034 1.819671 2.790473
3.639972
O 31 2.664555 3.100779 3.022511 3.121946 4.478727
5.323793
H 32 3.601643 3.915717 3.566346 3.584044 4.947546
5.743669
1
0
H 13 N 14 C 15 C 16 O 17
N 18
------------------------------------------------------------------------------
H 13 0.000000
N 14 2.132384 0.000000
C 15 3.183748 1.389999 0.000000
C 16 4.556414 2.550907 1.419695 0.000000
O 17 5.222557 3.093513 2.391356 1.230610 0.000000
N 18 5.458836 3.687143 2.329153 1.399627 2.277257
0.000000
H 19 6.414782 4.552249 3.246395 2.060920 2.477761
1.000576
C 20 5.423246 4.079423 2.720549 2.467791 3.563342
1.379652
N 21 6.697353 5.420114 4.057704 3.635386 4.581003
2.307532
H 22 7.530618 6.080734 4.692116 3.989581 4.727962
2.589986
H 23 6.949382 5.941255 4.645208 4.459167 5.488697
3.215805
N 24 4.471482 3.590576 2.459896 2.918311 4.144102
2.385438
C 25 3.203893 2.264559 1.370310 2.408059 3.581697
2.603873
C 26 3.894713 5.544403 5.864328 7.211909 8.252905
7.463767
H 27 4.130054 6.024425 6.544500 7.935052 8.902684
8.315991
C 28 2.913222 4.354018 4.653573 5.995392 7.012705
6.314762
H 29 2.742958 4.393719 4.937433 6.295942 7.197571
6.788655
H 30 3.690729 4.745617 4.778522 5.998956 7.078974
6.120605
O 31 5.135693 6.565663 6.657271 7.909519 9.031241
7.936752
H 32 5.527953 6.967952 7.077458 8.316515 9.423463
8.345508
0
H 19 C 20 N 21 H 22 H 23
N 24
------------------------------------------------------------------------------
H 19 0.000000
C 20 2.043456 0.000000
N 21 2.449328 1.340691 0.000000
H 22 2.315444 2.108614 1.010134 0.000000
H 23 3.453965 2.006962 1.009846 1.717434 0.000000
N 24 3.257328 1.330161 2.320197 3.271512 2.481451
0.000000
C 25 3.603046 2.232690 3.493826 4.340238 3.815440
1.360340
C 26 8.446115 6.680654 7.515089 8.520872 7.218069
5.353615
H 27 9.309864 7.625021 8.520716 9.521008 8.264070
6.309893
C 28 7.299684 5.643185 6.584787 7.568071 6.419867
4.358146
H 29 7.768525 6.280793 7.303924 8.255440 7.228201
5.067762
H 30 7.064913 5.312646 6.113744 7.094448 5.860634
4.053904
O 31 8.875737 6.964069 7.586353 8.592483 7.118497
5.652159
H 32 9.273624 7.381425 7.982500 8.977125 7.508068
6.095060
1
0
C 25 C 26 H 27 C 28 H 29
H 30
------------------------------------------------------------------------------
C 25 0.000000
C 26 4.899536 0.000000
H 27 5.719604 1.090083 0.000000
C 28 3.762169 1.529800 2.154441 0.000000
H 29 4.289226 2.154461 2.258482 1.089934 0.000000
H 30 3.739724 2.154462 2.894734 1.089760 1.779423
0.000000
O 31 5.517233 1.420155 2.073502 2.378389 3.084228
2.342773
H 32 5.965055 2.022249 2.375095 2.654240 3.120385
2.407829
0
O 31 H 32
------------------------------
O 31 0.000000
H 32 0.960209 0.000000
CYCLE: 1 TIME: 0.3 TIME LEFT: 3599.5 GRAD.:316.663 HEAT:-57.24264
CYCLE: 2 TIME: 0.2 TIME LEFT: 3599.3 GRAD.:373.870 HEAT:-61.11452
CYCLE: 3 TIME: 0.1 TIME LEFT: 3599.3 GRAD.:350.575 HEAT:-62.73094
CYCLE: 4 TIME: 0.2 TIME LEFT: 3599.0 GRAD.:406.336 HEAT:-72.28105
CYCLE: 5 TIME: 0.1 TIME LEFT: 3599.0 GRAD.:370.319 HEAT:-73.22361
CYCLE: 6 TIME: 0.2 TIME LEFT: 3598.8 GRAD.:133.942 HEAT:-75.98350
CYCLE: 7 TIME: 0.1 TIME LEFT: 3598.7 GRAD.: 97.023 HEAT:-76.70549
CYCLE: 8 TIME: 0.2 TIME LEFT: 3598.5 GRAD.: 63.559 HEAT:-77.70432
CYCLE: 9 TIME: 0.1 TIME LEFT: 3598.4 GRAD.: 66.277 HEAT:-78.34151
CYCLE: 10 TIME: 0.2 TIME LEFT: 3598.2 GRAD.: 86.535 HEAT:-79.64853
CYCLE: 11 TIME: 0.2 TIME LEFT: 3598.0 GRAD.: 84.361 HEAT:-80.14912
CYCLE: 12 TIME: 0.2 TIME LEFT: 3597.8 GRAD.:100.907
HEAT:-80.29683
CYCLE: 13 TIME: 0.2 TIME LEFT: 3597.7 GRAD.:106.462 HEAT:-80.50473
CYCLE: 14 TIME: 0.2 TIME LEFT: 3597.5 GRAD.: 88.719 HEAT:-80.75461
CYCLE: 15 TIME: 0.1 TIME LEFT: 3597.4 GRAD.: 66.306 HEAT:-80.89671
CYCLE: 16 TIME: 0.2 TIME LEFT: 3597.2 GRAD.: 58.719 HEAT:-81.31301
0TEST ON X SATISFIED
HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN 0.10
CYCLE: 17 TIME: 0.1 TIME LEFT: 3597.2 GRAD.: 59.008 HEAT:-81.32671
CYCLE: 18 TIME: 0.2 TIME LEFT: 3596.9 GRAD.: 52.349 HEAT:-81.70188
CYCLE: 19 TIME: 0.2 TIME LEFT: 3596.8 GRAD.: 33.008 HEAT:-81.88593
CYCLE: 20 TIME: 0.1 TIME LEFT: 3596.7 GRAD.: 27.248 HEAT:-81.95138
CYCLE: 21 TIME: 0.2 TIME LEFT: 3596.4 GRAD.: 34.463 HEAT:-82.21756
CYCLE: 22 TIME: 0.1 TIME LEFT: 3596.3 GRAD.: 33.912 HEAT:-82.22881
CYCLE: 23 TIME: 0.2 TIME LEFT: 3596.1 GRAD.: 22.517 HEAT:-82.42772
CYCLE: 24 TIME: 0.1 TIME LEFT: 3596.0 GRAD.: 21.215 HEAT:-82.43927
CYCLE: 25 TIME: 0.2 TIME LEFT: 3595.8 GRAD.: 15.506 HEAT:-82.57639
0TEST ON X SATISFIED
HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN 0.10
CYCLE: 26 TIME: 0.1 TIME LEFT: 3595.7 GRAD.: 15.129 HEAT:-82.58114
CYCLE: 27 TIME: 0.3 TIME LEFT: 3595.4 GRAD.: 21.441 HEAT:-82.58839
0TEST ON X SATISFIED
HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN 0.10
CYCLE: 28 TIME: 0.1 TIME LEFT: 3595.3 GRAD.: 20.116 HEAT:-82.59060
CYCLE: 29 TIME: 0.2 TIME LEFT: 3595.1 GRAD.: 20.398 HEAT:-82.59798
CYCLE: 30 TIME: 0.2 TIME LEFT: 3594.9 GRAD.: 25.249 HEAT:-82.60718
CYCLE: 31 TIME: 0.2 TIME LEFT: 3594.7 GRAD.: 28.399 HEAT:-82.61996
CYCLE: 32 TIME: 0.2 TIME LEFT: 3594.6 GRAD.: 17.864 HEAT:-82.63648
CYCLE: 33 TIME: 0.2 TIME LEFT: 3594.4 GRAD.: 17.140 HEAT:-82.65422
CYCLE: 34 TIME: 0.2 TIME LEFT: 3594.2 GRAD.: 12.469 HEAT:-82.68026
0TEST ON X SATISFIED
HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN 0.10
CYCLE: 35 TIME: 0.1 TIME LEFT: 3594.1 GRAD.: 12.037 HEAT:-82.68366
CYCLE: 36 TIME: 0.2 TIME LEFT: 3593.9 GRAD.: 15.773 HEAT:-82.71233
0TEST ON X SATISFIED
HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN 0.10
THERE HAVE BEEN 3 ATTEMPTS TO REDUCE THE GRADIENT.
DURING THESE ATTEMPTS THE ENERGY DROPPED BY LESS THAN 0.3000
KCAL/MOLE
FURTHER CALCULATION IS NOT JUSTIFIED AT THIS POINT.
ALL CONVERGERS ARE NOW FORCED ON
SHIFT=10, PULAY ON, CAMP-KING ON
AND ITERATION COUNTER RESET
"""""""""""""UNABLE TO ACHIEVE SELF-CONSISTENCE
DELTAE= NAN DELTAP= NAN
-------------------------------------------------------------------------------
AM1 MMOK GEO-OK CHARGE=0
remark line goes here
A FAILURE HAS OCCURRED, TREAT RESULTS WITH CAUTION!!
++++----**** FAILED TO ACHIEVE SCF. ****----++++
AM1 CALCULATION
VERSION 5.010
9-Feb-04
FOR SOME REASON THE SCF CALCULATION FAILED.
THE RESULTS WOULD BE MEANINGLESS, SO WILL NOT BE PRINTED.
TRY TO FIND THE REASON FOR THE FAILURE BY USING "PL".
CHECK YOUR GEOMETRY AND ALSO TRY USING SHIFT OR PULAY.
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA
NB NC
1 H
2 O 0.96446 * 1
3 C 1.41914 * 106.62490 * 2 1
4 H 1.12302 * 110.07806 * 57.87297 * 3
2 1
5 H 1.12314 * 109.40091 * 297.13667 * 3
2 1
6 C 1.52754 * 109.47041 * 177.85204 * 3
2 1
7 H 1.12618 * 109.18502 * 156.73428 * 6
3 2
8 O 1.43111 * 110.89091 * 272.08471 * 6
3 2
9 C 1.43935 * 111.84614 * 108.97363 * 8
6 3
10 H 1.13141 * 104.85952 * 126.04434 * 9
8 6
11 N 1.44484 * 110.43292 * 241.95546 * 9
8 6
12 C 1.41945 * 127.93475 * 69.92530 * 11
9 8
13 H 1.09921 * 120.57298 * 3.63582 * 12
11 9
14 N 1.34338 * 113.52278 * 183.58483 * 12
11 9
15 C 1.39887 * 104.63624 * 1.28719 * 14
12 11
16 C 1.44904 * 129.84272 * 180.17303 * 15
14 12
17 O 1.23818 * 129.20255 * 0.18826 * 16
15 14
18 N 1.42204 * 112.90281 * 180.03754 * 16
15 14
19 H 0.99780 * 116.27668 * 182.92594 * 18
16 15
20 C 1.40729 * 123.99566 * 359.92462 * 18
16 15
21 N 1.41513 * 117.51896 * 184.37320 * 20
18 16
22 H 0.99614 * 115.07538 * 320.82530 * 21
20 18
23 H 0.99833 * 114.26203 * 186.44393 * 21
20 18
24 N 1.35603 * 123.80478 * 0.69728 * 20
18 16
25 C 1.38373 * 114.34721 * -1.20406 * 24
20 18
26 C 1.54455 * 113.33165 * 32.38328 * 6
3 2
27 H 1.12214 * 111.42845 * 14.96621 * 26
6 3
28 C 1.53191 * 105.56070 * 254.41860 * 26
6 3
29 H 1.11917 * 109.57468 * 107.73993 * 28
26 6
30 H 1.11300 * 111.60341 * 228.74673 * 28
26 6
31 O 1.41976 * 106.60242 * 134.84610 * 26
6 3
32 H 0.96454 * 106.88060 * 181.48869 * 31
26 6
Does anyone have an idea how to get this going?
Thanks a lot again,
Carsten
--
Carsten Detering
University of Washington
Department of Chemistry
Box 351700
Seattle, WA 98195-1700
Fon 206.543.5081
Fax 206.685.8665
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Received on Mon Feb 09 2004 - 20:53:00 PST
