Hi Francois! Thanks very much for the information. :) I will do as you have
suggested. it is good advice.
best regards,
gt
On 12 January 2012 17:57, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 - 10:30:02 PST
