Hi,
I am trying to parametrise the inhibitor darunavir using red 3 and gaussian
03.
http://www.chemspider.com/Chemical-Structure.184733.html?rid=1be99119-5c50-4194-bd92-2e9ad69b0ab6
I added the hydrogens using openbabel to a pdb of the ligand. It correctly
added them, including two hydrogens to the primary amine (N38 in the pdb)
in a trigonal planar geometry. I believe this is the correct geometry as
the nitrogen is positioned near a conjugate system and its lone pair should
delocalise into the adjacent aligned p-orbitals.
however, upon using ante red and red 3 to interface with gaussian, the
resulting mol2 file indicates that the nitrogen has a tetrahedral geometry.
I'm sure this is not correct. is there a method to specify that it should
be planar?
Any help would be greatly appreciated.
Best regards,
gt
my red 3 settings are as follows:
#----------- Variables that can be modified in R.E.D.: See HowTo.pdf as
well ------------
$XRED = "Off"; # If XRED="ON", R.E.D. will be executed using the XRED
graphical interface.
$NP = "8"; # Number of cpu(s)/core(s) used in parallel in QM
calculations.
$QMSOFT = "Gaussian"; # "GAMESS-US" (GAMESS-US or WinGAMESS), "PC-GAMESS",
or "GAUSSIAN" (g09, g03, g98 or g94) is used in QM calculations.
$DIR = "Data"; # Directory name where the final data will be stored.
$OPT_Calc = "ON"; # Geometry optimization will be carried out only if
$OPT_Calc = "ON".
$MEPCHR_Calc = "On"; # MEP computation & charge fitting will be carried
out if $MEPCHR_Calc = "ON".
$Re_Fit = "Off"; # Charges are re-fitted & force field libraries re-built
from a previous R.E.D. job.
$CHR_TYP = "RESP-A1"; # Charge derivation models: "RESP-A1, RESP-A2,
RESP-C1, RESP-C2, ESP-A1, ESP-A2, ESP-C1, ESP-C2".
#######################
##################################################################
The input pdb is:
HETATM 26 O1 DAR A1200 24.413 25.475 11.833 1.00 0.00 A1
O
HETATM 27 C2 DAR A1200 23.493 25.227 10.779 1.00 0.00 A1
C
HETATM 63 H2 DAR A1200 24.007 24.792 9.947 1.00 0.00 A1
H
HETATM 28 O3 DAR A1200 22.483 24.363 11.236 1.00 0.00 A1
O
HETATM 29 CT4 DAR A1200 21.193 25.063 11.296 1.00 0.00 A1
C
HETATM 64 H4 DAR A1200 20.981 25.380 12.296 1.00 0.00 A1
H
HETATM 65 H4 DAR A1200 20.378 24.437 10.998 1.00 0.00 A1
H
HETATM 30 CT5 DAR A1200 21.363 26.256 10.383 1.00 0.00 A1
C
HETATM 66 H5 DAR A1200 20.815 27.097 10.754 1.00 0.00 A1
H
HETATM 67 H5 DAR A1200 20.995 26.067 9.396 1.00 0.00 A1
H
HETATM 31 C6 DAR A1200 22.839 26.537 10.396 1.00 0.00 A1
C
HETATM 68 H6 DAR A1200 23.077 26.959 9.442 1.00 0.00 A1
H
HETATM 24 C7 DAR A1200 23.321 27.511 11.496 1.00 0.00 A1
C
HETATM 60 H7 DAR A1200 23.349 28.527 11.161 1.00 0.00 A1
H
HETATM 25 CT8 DAR A1200 24.640 26.896 11.912 1.00 0.00 A1
C
HETATM 61 H8 DAR A1200 24.894 27.184 12.911 1.00 0.00 A1
H
HETATM 62 H8 DAR A1200 25.452 27.215 11.293 1.00 0.00 A1
H
HETATM 23 O9 DAR A1200 22.469 27.402 12.655 1.00 0.00 A1
O
HETATM 21 C10 DAR A1200 21.566 28.405 12.887 1.00 0.00 A1
C
HETATM 22 O11 DAR A1200 21.634 29.442 12.299 1.00 0.00 A1
O
HETATM 20 N12 DAR A1200 20.709 28.031 13.805 1.00 0.00 A1
N
HETATM 59 H12 DAR A1200 20.804 27.130 14.191 1.00 0.00 A1
H
HETATM 19 C13 DAR A1200 19.599 28.895 14.297 1.00 0.00 A1
C
HETATM 58 H13 DAR A1200 19.468 29.787 13.721 1.00 0.00 A1
H
HETATM 32 CT14DAR A1200 18.307 28.149 14.166 1.00 0.00 A1
C
HETATM 69 H14 DAR A1200 17.511 28.780 14.504 1.00 0.00 A1
H
HETATM 70 H14 DAR A1200 18.384 27.261 14.757 1.00 0.00 A1
H
HETATM 38 C15 DAR A1200 18.024 27.733 12.757 1.00 0.00 A1
C
HETATM 33 C16 DAR A1200 18.054 26.400 12.363 1.00 0.00 A1
C
HETATM 71 H16 DAR A1200 18.248 25.672 13.068 1.00 0.00 A1
H
HETATM 34 C17 DAR A1200 17.831 26.025 11.051 1.00 0.00 A1
C
HETATM 72 H17 DAR A1200 17.841 25.027 10.790 1.00 0.00 A1
H
HETATM 35 C18 DAR A1200 17.597 26.981 10.098 1.00 0.00 A1
C
HETATM 73 H18 DAR A1200 17.457 26.709 9.112 1.00 0.00 A1
H
HETATM 36 C19 DAR A1200 17.550 28.293 10.460 1.00 0.00 A1
C
HETATM 74 H19 DAR A1200 17.351 29.011 9.746 1.00 0.00 A1
H
HETATM 37 C20 DAR A1200 17.765 28.674 11.767 1.00 0.00 A1
C
HETATM 75 H20 DAR A1200 17.733 29.675 12.015 1.00 0.00 A1
H
HETATM 17 C21 DAR A1200 19.962 29.337 15.738 1.00 0.00 A1
C
HETATM 56 H21 DAR A1200 20.951 29.744 15.689 1.00 0.00 A1
H
HETATM 18 O22 DAR A1200 19.895 28.206 16.604 1.00 0.00 A1
O
HETATM 57 H22 DAR A1200 18.987 27.866 16.622 1.00 0.00 A1
H
HETATM 16 CT23DAR A1200 19.063 30.433 16.294 1.00 0.00 A1
C
HETATM 54 H23 DAR A1200 18.039 30.153 16.156 1.00 0.00 A1
H
HETATM 55 H23 DAR A1200 19.273 30.559 17.336 1.00 0.00 A1
H
HETATM 11 N24 DAR A1200 19.316 31.708 15.598 1.00 0.00 A1
N
HETATM 12 CT25DAR A1200 20.128 32.699 16.353 1.00 0.00 A1
C
HETATM 45 H25 DAR A1200 19.744 32.758 17.350 1.00 0.00 A1
H
HETATM 46 H25 DAR A1200 20.052 33.626 15.825 1.00 0.00 A1
H
HETATM 13 C26 DAR A1200 21.628 32.355 16.432 1.00 0.00 A1
C
HETATM 47 H26 DAR A1200 21.764 31.376 16.841 1.00 0.00 A1
H
HETATM 15 CT27DAR A1200 22.282 33.401 17.329 1.00 0.00 A1
C
HETATM 51 H27 DAR A1200 22.138 34.373 16.907 1.00 0.00 A1
H
HETATM 52 H27 DAR A1200 23.330 33.198 17.408 1.00 0.00 A1
H
HETATM 53 H27 DAR A1200 21.838 33.365 18.302 1.00 0.00 A1
H
HETATM 14 CT28DAR A1200 22.279 32.317 15.034 1.00 0.00 A1
C
HETATM 48 H28 DAR A1200 22.177 33.274 14.567 1.00 0.00 A1
H
HETATM 49 H28 DAR A1200 21.795 31.574 14.435 1.00 0.00 A1
H
HETATM 50 H28 DAR A1200 23.317 32.076 15.130 1.00 0.00 A1
H
HETATM 8 S29 DAR A1200 18.136 32.331 14.660 1.00 0.00 A1
S
HETATM 9 O30 DAR A1200 18.756 33.247 13.785 1.00 0.00 A1
O
HETATM 10 O31 DAR A1200 17.453 31.221 14.098 1.00 0.00 A1
O
HETATM 5 C32 DAR A1200 17.012 33.220 15.616 1.00 0.00 A1
C
HETATM 4 C33 DAR A1200 17.180 34.513 15.867 1.00 0.00 A1
C
HETATM 42 H33 DAR A1200 17.966 35.041 15.457 1.00 0.00 A1
H
HETATM 3 C34 DAR A1200 16.193 35.169 16.760 1.00 0.00 A1
C
HETATM 41 H34 DAR A1200 16.219 36.186 16.931 1.00 0.00 A1
H
HETATM 2 C35 DAR A1200 15.195 34.330 17.380 1.00 0.00 A1
C
HETATM 7 C36 DAR A1200 14.979 33.107 17.003 1.00 0.00 A1
C
HETATM 44 H36 DAR A1200 14.125 32.610 17.302 1.00 0.00 A1
H
HETATM 6 C37 DAR A1200 15.919 32.472 16.187 1.00 0.00 A1
C
HETATM 43 H37 DAR A1200 15.831 31.462 15.992 1.00 0.00 A1
H
HETATM 1 N38 DAR A1200 14.279 34.925 18.220 1.00 0.00 A1
N
HETATM 39 H38 DAR A1200 14.417 35.852 18.522 1.00 0.00 A1
H
HETATM 40 H38 DAR A1200 13.486 34.423 18.518 1.00 0.00 A1
H
TER
END
##################################################################
and the output mol2 file is:
.<TRIPOS>MOLECULE
DAR
75 78 1 0 1
SMALL
USER_CHARGES
.<TRIPOS>ATOM
1 O1 6.574581 1.691304 0.773791 O 1 DAR
-0.4131 ****
2 C2 6.829592 0.860311 -0.323095 C 1 DAR
0.4023 ****
3 H2 7.699699 1.226284 -0.853467 H 1 DAR
0.0362 ****
4 O3 7.094910 -0.429178 0.076830 O 1 DAR
-0.4445 ****
5 CT4 5.901221 -1.182994 0.050180 C 1 DAR
0.1040 ****
6 H4 5.336271 -1.025455 0.961415 H 1 DAR
0.0746 ****
7 H4 6.171384 -2.226874 -0.019585 H 1 DAR
0.0746 ****
8 CT5 5.157103 -0.655243 -1.173610 C 1 DAR
-0.2182 ****
9 H5 4.095635 -0.852008 -1.156546 H 1 DAR
0.0934 ****
10 H5 5.563946 -1.114346 -2.067951 H 1 DAR
0.0934 ****
11 C6 5.523202 0.834719 -1.160866 C 1 DAR
0.0116 ****
12 H6 5.686839 1.214182 -2.161645 H 1 DAR
0.0304 ****
13 C7 4.584753 1.802808 -0.416181 C 1 DAR
0.0732 ****
14 H7 4.003592 2.412757 -1.086695 H 1 DAR
0.1029 ****
15 CT8 5.566272 2.597397 0.431420 C 1 DAR
0.0410 ****
16 H8 5.122683 2.986865 1.335510 H 1 DAR
0.0700 ****
17 H8 5.971587 3.425519 -0.148676 H 1 DAR
0.0700 ****
18 O9 3.698492 1.142612 0.478837 O 1 DAR
-0.3238 ****
19 C10 2.468163 0.853928 0.053666 C 1 DAR
0.5902 ****
20 O11 2.071276 1.086959 -1.052010 O 1 DAR
-0.5654 ****
21 N12 1.758499 0.273823 1.036619 N 1 DAR
-0.3155 ****
22 H12 2.184952 0.216019 1.933628 H 1 DAR
0.2356 ****
23 C13 0.392705 -0.187195 0.874256 C 1 DAR
0.1241 ****
24 H13 0.161362 -0.111231 -0.175534 H 1 DAR
0.1152 ****
25 CT1 0.287564 -1.658744 1.314582 C 1 DAR
-0.0640 ****
26 H14 -0.742692 -1.979570 1.220731 H 1 DAR
0.0417 ****
27 H14 0.560620 -1.737418 2.363626 H 1 DAR
0.0417 ****
28 C15 1.170689 -2.597633 0.517307 C 1 DAR
0.0183 ****
29 C16 2.286540 -3.188347 1.095582 C 1 DAR
-0.2110 ****
30 H16 2.528567 -2.978718 2.123596 H 1 DAR
0.1359 ****
31 C17 3.093956 -4.052801 0.370456 C 1 DAR
-0.1218 ****
32 H17 3.950169 -4.504389 0.840009 H 1 DAR
0.1271 ****
33 C18 2.794738 -4.335015 -0.950867 C 1 DAR
-0.1551 ****
34 H18 3.417318 -5.005177 -1.516703 H 1 DAR
0.1367 ****
35 C19 1.681753 -3.751382 -1.538040 C 1 DAR
-0.1738 ****
36 H19 1.438580 -3.967797 -2.563147 H 1 DAR
0.1440 ****
37 C20 0.874816 -2.893203 -0.810962 C 1 DAR
-0.0429 ****
38 H20 0.008217 -2.454991 -1.271838 H 1 DAR
0.0909 ****
39 C21 -0.538667 0.760274 1.650966 C 1 DAR
0.1138 ****
40 H21 -0.231992 1.762748 1.398382 H 1 DAR
0.1089 ****
41 O22 -0.324874 0.660395 3.042042 O 1 DAR
-0.6673 ****
42 H22 -0.647208 -0.170779 3.363439 H 1 DAR
0.4217 ****
43 CT2 -2.043995 0.636886 1.375616 C 1 DAR
-0.0439 ****
44 H23 -2.373597 -0.375678 1.564290 H 1 DAR
0.0582 ****
45 H23 -2.546609 1.269022 2.098398 H 1 DAR
0.0582 ****
46 N24 -2.451254 1.061763 0.032374 N 1 DAR
-0.1758 ****
47 CT2 -3.045710 2.403549 -0.080427 C 1 DAR
-0.0980 ****
48 H25 -3.816504 2.512539 0.679770 H 1 DAR
0.0876 ****
49 H25 -3.521068 2.475391 -1.046362 H 1 DAR
0.0876 ****
50 C26 -2.039136 3.554137 0.034080 C 1 DAR
0.1361 ****
51 H26 -1.527171 3.479151 0.989751 H 1 DAR
0.0431 ****
52 CT2 -2.808733 4.879619 0.033222 C 1 DAR
-0.3350 ****
53 H27 -3.353691 5.014985 -0.897537 H 1 DAR
0.0818 ****
54 H27 -2.127603 5.717336 0.139074 H 1 DAR
0.0818 ****
55 H27 -3.523656 4.930074 0.849651 H 1 DAR
0.0818 ****
56 CT2 -1.002023 3.521156 -1.090229 C 1 DAR
-0.0867 ****
57 H28 -1.485291 3.615405 -2.058686 H 1 DAR
0.0256 ****
58 H28 -0.430244 2.602459 -1.098234 H 1 DAR
0.0256 ****
59 H28 -0.304584 4.346889 -0.985171 H 1 DAR
0.0256 ****
60 S29 -3.030716 -0.090729 -0.992845 S 1 DAR
0.7455 ****
61 O30 -3.106223 0.505691 -2.289359 O 1 DAR
-0.4926 ****
62 O31 -2.230138 -1.258932 -0.765870 O 1 DAR
-0.4636 ****
63 C32 -4.676685 -0.489481 -0.497436 C 1 DAR
0.0688 ****
64 C33 -5.751388 0.237910 -0.996291 C 1 DAR
-0.1971 ****
65 H33 -5.582586 1.019749 -1.711691 H 1 DAR
0.1739 ****
66 C34 -7.036871 -0.060051 -0.600637 C 1 DAR
-0.1826 ****
67 H34 -7.861927 0.507951 -0.992281 H 1 DAR
0.1512 ****
68 C35 -7.278660 -1.102304 0.297752 C 1 DAR
0.3367 ****
69 C36 -6.196085 -1.840729 0.780112 C 1 DAR
-0.1801 ****
70 H36 -6.367745 -2.656396 1.459837 H 1 DAR
0.1537 ****
71 C37 -4.911264 -1.538804 0.382589 C 1 DAR
-0.2463 ****
72 H37 -4.091266 -2.135281 0.733515 H 1 DAR
0.1949 ****
73 N38 -8.562083 -1.374502 0.727717 N 1 DAR
-0.9174 ****
74 H38 -9.298097 -1.066169 0.131336 H 1 DAR
0.3975 ****
75 H38 -8.719872 -2.292364 1.081384 H 1 DAR
0.3975 ****
.<TRIPOS>BOND
1 1 2 1
2 1 15 1
3 2 3 1
4 2 4 1
5 2 11 1
6 4 5 1
7 5 6 1
8 5 7 1
9 5 8 1
10 8 9 1
11 8 10 1
12 8 11 1
13 11 12 1
14 11 13 1
15 13 14 1
16 13 15 1
17 13 18 1
18 15 16 1
19 15 17 1
20 18 19 1
21 19 20 1
22 19 21 1
23 21 22 1
24 21 23 1
25 23 24 1
26 23 25 1
27 23 39 1
28 25 26 1
29 25 27 1
30 25 28 1
31 28 29 1
32 28 37 1
33 29 30 1
34 29 31 1
35 31 32 1
36 31 33 1
37 33 34 1
38 33 35 1
39 35 36 1
40 35 37 1
41 37 38 1
42 39 40 1
43 39 41 1
44 39 43 1
45 41 42 1
46 43 44 1
47 43 45 1
48 43 46 1
49 46 47 1
50 46 60 1
51 47 48 1
52 47 49 1
53 47 50 1
54 50 51 1
55 50 52 1
56 50 56 1
57 52 53 1
58 52 54 1
59 52 55 1
60 56 57 1
61 56 58 1
62 56 59 1
63 60 61 1
64 60 62 1
65 60 63 1
66 63 64 1
67 63 71 1
68 64 65 1
69 64 66 1
70 66 67 1
71 66 68 1
72 68 69 1
73 68 73 1
74 69 70 1
75 69 71 1
76 71 72 1
77 73 74 1
78 73 75 1
.<TRIPOS>SUBSTRUCTURE
1 DAR 1 **** 0 **** ****
#########################################################
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Received on Thu Jan 12 2012 - 03:30:02 PST
