Subject: Re: CCL:MOPAC format from mol file

From: andre mauricio de oliveira <[email-masked]>
Date: Fri, 11 Apr 2003 09:23:06 -0300 (BSC)

dear Dr Manzetti,

You should replace `KEYWORDS GO HERE`  for the suitable keywords needed
for your calculus (see keywords list in MOPAC manual).

Regards.

On Thu, 10 Apr 2003, Sergio Manzetti wrote:

> Hi, I try to generate a MOPAC calculation of NADP, but when I try with the input file it says unrecognized keyword, or atom ill defined...below is the MOPAC input for NADP, can anyone see something missing? Thanks.
>
> Sergio
>
> KEYWORDS GO HERE
> C 0.0000000 0 0.000000 0 0.000000 0 0 0 0 0.0000
> C 1.4909987 1 0.000000 0 0.000000 0 1 0 0 0.0000
> C 1.4589154 1 120.833751 1 0.000000 0 1 2 0 0.0000
> C 1.5952887 1 104.179711 1 -123.629997 1 1 2 3 0.0000
> C 1.4327690 1 118.649162 1 -177.109970 1 4 1 2 0.0000
> C 1.4961080 1 107.216845 1 -161.441326 1 5 4 1 0.0000
> C 1.4141955 1 113.692259 1 -69.678566 1 6 5 4 0.0000
> C 1.4861497 1 114.497941 1 51.716667 1 6 5 4 0.0000
> C 1.4452941 1 111.437239 1 74.248685 1 8 6 5 0.0000
> C 1.5054733 1 103.365827 1 -166.496868 1 8 6 5 0.0000
> C 1.4574546 1 111.809306 1 -86.763311 1 10 8 6 0.0000
> C 1.4501824 1 106.004635 1 161.480085 1 7 6 5 0.0000
> C 1.4742222 1 107.653685 1 -139.809374 1 12 7 6 0.0000
> C 1.3833969 1 128.944472 1 66.940975 1 13 12 7 0.0000
> C 1.2992633 1 112.520808 1 178.715024 1 14 13 12 0.0000
> C 1.3880497 1 104.385214 1 -0.091869 1 15 14 13 0.0000
> C 1.4212055 1 132.803663 1 -178.929926 1 16 15 14 0.0000
> C 1.3238100 1 121.797140 1 0.190214 1 17 16 15 0.0000
> C 1.3672524 1 118.021273 1 -179.725459 1 17 16 15 0.0000
> C 1.3491634 1 120.848602 1 -0.066268 1 19 17 16 0.0000
> C 1.3502274 1 125.054262 1 -0.679602 1 20 19 17 0.0000
> C 1.3539457 1 111.183849 1 0.730735 1 16 15 14 0.0000
> O 1.5778419 1 110.549256 1 126.272978 1 1 2 3 0.0000
> N 1.5977684 1 134.654605 1 -121.941769 1 23 1 2 0.0000
> N 1.4758096 1 110.162467 1 -56.814322 1 24 23 1 0.0000
> N 1.5009081 1 105.285562 1 72.156186 1 24 23 1 0.0000
> N 1.5660166 1 104.006219 1 -178.870480 1 24 23 1 0.0000
> N 1.4258156 1 118.281226 1 69.379294 1 27 24 23 0.0000
> N 1.5245626 1 111.272573 1 175.371156 1 28 27 24 0.0000
> N 1.4342420 1 110.854111 1 -60.335961 1 29 28 27 0.0000
> N 1.5326307 1 114.247710 1 57.889983 1 29 28 27 0.0000
> N 1.4234219 1 112.607565 1 144.895209 1 31 29 28 0.0000
> N 1.5163852 1 105.507122 1 -95.103814 1 31 29 28 0.0000
> N 1.4066321 1 113.843089 1 -150.480848 1 33 31 29 0.0000
> N 1.4146388 1 111.185567 1 114.063306 1 30 29 28 0.0000
> N 1.4537538 1 111.078782 1 -139.680558 1 35 30 29 0.0000
> N 1.4161479 1 118.169858 1 79.144271 1 36 35 30 0.0000
> N 1.4306551 1 116.150232 1 -179.373873 1 37 36 35 0.0000
> N 1.4574762 1 121.740928 1 -178.042998 1 38 37 36 0.0000
> N 1.2482388 1 120.855729 1 167.276205 1 39 38 37 0.0000
> N 1.3598312 1 121.250981 1 -10.757352 1 39 38 37 0.0000
> N 1.4154049 1 118.632746 1 0.854415 1 38 37 36 0.0000
> N 1.3635670 1 123.585731 1 -1.005756 1 42 38 37 0.0000
> N 1.3617566 1 118.413749 1 0.448534 1 43 42 38 0.0000
> C 1.6104652 1 123.853336 1 -145.123171 1 11 10 8 0.0000
> C 1.5048751 1 109.327762 1 -91.096377 1 45 11 10 0.0000
> C 1.5109020 1 102.991438 1 29.325753 1 45 11 10 0.0000
> C 1.4871210 1 100.481918 1 147.314143 1 45 11 10 0.0000
>
>

Andre Mauricio de Oliveira

VOICE +55-031-374-1325
      +55-031-499-5765
FAX   +55-031-499-5700

Laboratorio de QSAR e Modelagem Molecular
Nucleo de Estudos em Quimica Medicinal (NEQUIM)
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Departamento de Quimica ICEx
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Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901
Belo Horizonte MG Brazil

---

From: "Tamas E. Gunda" <[email-masked]>
Date: Fri, 11 Apr 2003 09:16:26 +0200

MOPAC files begin with three data lines, the first is for the key words, which say to the program what to do, how to do etc, consult with the MOPAC or target program documentation.

The next two lines may contain additional info, then the coordinate section follows:

EF GNORM=0.100 MMOK GEO-OK AM1 MULLIK PULAY
.
.
  C    0.000000  0    0.000000  0    0.000000  0    0   0   0
  C    1.408173  1    0.000000  0    0.000000  0    1   0   0
  C    1.389786  1  119.080032  1    0.000000  0    2   1   0
  C    1.397278  1  120.531311  1    0.000000  1    3   2   1
....

By the way, you coordinates look somehow corrupted, they contain two molecules and a lonely O atom (H2O?), all the atoms of the second one are N atoms.

With regards

Tamas E. Gunda

----------------------------------------------
Prof. Tamas E. Gunda
Department of Pharmaceutical Chemistry
Medical and Health Center
University of Debrecen, POBox 36
H-4010 Debrecen, Hungary
[email-masked]

  ----- Original Message ----- 
  From: Sergio Manzetti 
  To: [email-masked] 
  Sent: Thursday, April 10, 2003 19:46
  Subject: CCL:MOPAC format from mol file

  Sergio

KEYWORDS GO HEREC 0.0000000 0 0.000000 0 0.000000 0 0 0 0 0.0000C 1.4909987 1 0.000000 0 0.000000 0 1 0 0 0.0000C 1.4589154 1 120.833751 1 0.000000 0 1 2 0 0.0000C 1.5952887 1 104.179711 1 -123.629997 1 1 2 3 0.0000C 1.4327690 1 118.649162 1 -177.109970 1 4 1 2 0.0000C 1.4961080 1 107.216845 1 -161.441326 1 5 4 1 0.0000C 1.4141955 1 113.692259 1 -69.678566 1 6 5 4 0.0000C 1.4861497 1 114.497941 1 51.716667 1 6 5 4 0.0000C 1.4452941 1 111.437239 1 74.248685 1 8 6 5 0.0000C 1.5054733 1 103.365827 1 -166.496868 1 8 6 5 0.0000C 1.4574546 1 111.809306 1 -86.763311 1 10 8 6 0.0000C 1.4501824 1 106.004635 1 161.480085 1 7 6 5 0.0000C 1.4742222 1 107.653685 1 -139.809374 1 12 7 6 0.0000C 1.3833969 1 128.944472 1 66.940975 1 13 12 7 0.0000C 1.2992633 1 112.520808 1 178.715024 1 14 13 12 0.0000C 1.3880497 1 104.385214 1 -0.091869 1 15 14 13 0.0000C 1.4212055 1 132.803663 1 -178.929926 1 16 15 14 0.0000C 1.3238100 1 121.797140 1 0.190214 1 17 16 15 0.0000C 1.3672524 1 118.021273 1 -179.725459 1 17 16 15 0.0000C 1.3491634 1 120.848602 1 -0.066268 1 19 17 16 0.0000C 1.3502274 1 125.054262 1 -0.679602 1 20 19 17 0.0000C 1.3539457 1 111.183849 1 0.730735 1 16 15 14 0.0000O 1.5778419 1 110.549256 1 126.272978 1 1 2 3 0.0000N 1.5977684 1 134.654605 1 -121.941769 1 23 1 2 0.0000N 1.4758096 1 110.162467 1 -56.814322 1 24 23 1 0.0000N 1.5009081 1 105.285562 1 72.156186 1 24 23 1 0.0000N 1.5660166 1 104.006219 1 -178.870480 1 24 23 1 0.0000N 1.4258156 1 118.281226 1 69.379294 1 27 24 23 0.0000N 1.5245626 1 111.272573 1 175.371156 1 28 27 24 0.0000N 1.4342420 1 110.854111 1 -60.335961 1 29 28 27 0.0000N 1.5326307 1 114.247710 1 57.889983 1 29 28 27 0.0000N 1.4234219 1 112.607565 1 144.895209 1 31 29 28 0.0000N 1.5163852 1 105.507122 1 -95.103814 1 31 29 28 0.0000N 1.4066321 1 113.843089 1 -150.480848 1 33 31 29 0.0000N 1.4146388 1 111.185567 1 114.063306 1 30 29 28 0.0000N 1.4537538 1 111.078782 1 -139.680558 1 35 30 29 0.0000N 1.4161479 1 118.169858 1 79.144271 1 36 35 30 0.0000N 1.4306551 1 116.150232 1 -179.373873 1 37 36 35 0.0000N 1.4574762 1 121.740928 1 -178.042998 1 38 37 36 0.0000N 1.2482388 1 120.855729 1 167.276205 1 39 38 37 0.0000N 1.3598312 1 121.250981 1 -10.757352 1 39 38 37 0.0000N 1.4154049 1 118.632746 1 0.854415 1 38 37 36 0.0000N 1.3635670 1 123.585731 1 -1.005756 1 42 38 37 0.0000N 1.3617566 1 118.413749 1 0.448534 1 43 42 38 0.0000C 1.6104652 1 123.853336 1 -145.123171 1 11 10 8 0.0000C 1.5048751 1 109.327762 1 -91.096377 1 45 11 10 0.0000C 1.5109020 1 102.991438 1 29.325753 1 45 11 10 0.0000C 1.4871210 1 100.481918 1 147.314143 1 45 11 10 0.0000