Dear gt,
Several comments
-1 You used Ante_R.E.D. 1.x from the R.E.D. III.x tools: this version
of Ante_R.E.D. does not handle chemical equivalencing between
different chemical groups. This means that chemically equivalent atoms
will not bear the same charge value, and this is an error. Please, use
instead Ante_R.E.D. 2.0 . R.E.D. Server & this should solve your
problem.
Please see: http://q4md-forcefieldtools.org/REDS/news.php#2
An example of problem in your mol2 file is the two carbons of the two
methyl groups: they should bear the same charge value & it is not the
case...
See:
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
same problem for the 2 oxygens of the N-sulfo group
same problem for the 2 ortho carbons in the aniline aromatic ring
same problem for the 2 meta carbons in the aniline aromatic ring
etc... etc...
2- the atom names in your mol2 file are not correct; in the philosophy
of a force field library two atoms belonging to a given residue cannot
share the same name! please, once again use Ante_R.E.D. 2.0 & it
should correct redundant atom names in the PDB input file.
Please see
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
Do not provide CT atom names in the PDB input file; use regular atom
names in the PDB input file.
Please see
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
and ask new questions in the q4md-fft mailing if something is still not clear.
3- I looked at the geometry of your nitrogen atoms; they look all ok to me;
which nitrogen atom do you think has a wrong geometry? is it that of
'aniline': if so; it is between the sp3 and sp2 hybridizations & I
think this is normal...
See for instance the optimized geometry of the nucleosides in the W-78
R.E.DD.B. project: http://q4md-forcefieldtools.org/REDDB/projects/W-78/
(look at the Java applet of the mol2 files; remove the electrostatic
potential and charge values to better display the optimized geometry
by QM)
When you want to learn about RESP charge derivation, you could use
R.E.D. Server to generate data, provide the PXXXX code of your R.E.D.
Server job/test in the q4md-fft mailing list and ask your questions
from there. We can look at your data and efficiently help you...
I hope this helps.
regards, Francois
Quoting g t <sketchfoot.gmail.com>:
> 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 - 10:00:04 PST
