Your N1 is not protonated as it is in the paper.
On Wed, 25 Nov 2015 12:39:59 +0200
Fabian gmail <fabian.glaser.gmail.com> wrote:
> Thanks for the detailed answer
>
> Well I tried several times to run reduce and antechamber with
> different options (e.g. with -Xplor parameter in reduce) but the
> names are not identical not in the PDB, but more importantly not in
> the mol2 file. And the charges are very different. The authors do use
> GAFF but with RESP for partial charges….
>
> "Partial charges for ligands were obtained using RESP38 fi tting for
> the electrostatic potentials calculated using Gaussian0339 at the
> Hartree− Fock/6-31G* level of theory."
>
> As you can see the PDB indeed names the ligand correctly SKF, and so
> the sqm.pdb file, and indeed I used AM1-BCC charge method, but the
> charges and atoms types are indeed quite different, I paste both my
> results and their results for comparison…. I guess I will try anyway
> and see how different the results are.
>
> I guess the results will be different, but in any case I am looking
> for a certain degree of reproducibility before I start playing with
> my molecules, if the results are completely wrong well… I will
> rethink.
>
> THanks!!
>
> Fabian
>
>
> MY RESULTS
>
> .<TRIPOS>MOLECULE
> SKF
> 26 27 1 0 0
> SMALL
> bcc
>
>
> .<TRIPOS>ATOM
> 1 C4 28.3480 46.0370 16.7830 ca 3001 SKF
> -0.157000 2 C5 27.8990 45.5320 15.5700 ca 3001
> SKF -0.017000 3 C6 27.8220 44.1470 15.3850 ca
> 3001 SKF -0.387500 4 C7 28.1930 43.2860 16.4100
> ca 3001 SKF -0.010000 5 S 27.2610 43.4900
> 13.8470 sy 3001 SKF 1.528200 6 C8 28.6420
> 43.7900 17.6160 ca 3001 SKF -0.141300 7 C9
> 28.7200 45.1740 17.8070 ca 3001 SKF -0.008300 8
> O1 27.4850 44.4300 12.7700 o 3001 SKF -0.658800
> 9 O2 25.8660 43.1330 13.8730 o 3001 SKF
> -0.658800 10 N 28.1050 42.1870 13.5730 n3 3001
> SKF -1.026700 11 C1 28.9650 42.8430 18.7440 c3
> 3001 SKF 0.194100 12 C2 29.2110 44.8480 20.1940
> c3 3001 SKF 0.150800 13 C3 29.4880 45.7050
> 18.9780 c3 3001 SKF -0.087100 14 N1 29.7000
> 43.4830 19.8600 n3 3001 SKF -0.793200 15 HC32
> 30.4380 45.7060 18.7810 hc 3001 SKF 0.062700 16
> HC31 29.2340 46.6240 19.1540 hc 3001 SKF 0.062700
> 17 HC22 29.6670 45.1980 20.9750 h1 3001 SKF
> 0.059700 18 HC21 28.2630 44.8360 20.4000 h1 3001
> SKF 0.059700 19 HC12 28.1400 42.4640 19.0850 h1
> 3001 SKF 0.066200 20 HC11 29.4940 42.1070 18.3980
> h1 3001 SKF 0.066200 21 HN1 30.3490 43.1010
> 20.2760 hn 3001 SKF 0.353800 22 HC7 28.1370
> 42.3270 16.2790 ha 3001 SKF 0.153000 23 HC5
> 27.6400 46.1350 14.8560 ha 3001 SKF 0.152000 24
> HC4 28.4020 46.9960 16.9160 ha 3001 SKF 0.141000
> 25 H2N 27.9670 41.7280 12.8590 hn 3001 SKF
> 0.446800 26 H1N 28.7030 41.9350 14.1370 hn 3001
> SKF 0.446800 .<TRIPOS>BOND
>
>
> THEIR CHARGES AND ATOM TYPES
>
> Atom Name
> Atom Type
> Partial Charge
> O1
> S1
> O2
> N2
> H12
> H13
> C1
> C6
> H5
> C2
> H3
> C3
> H4
> C4
> C5
> C9
> H7
> H8
> N1
> H1
> H2
> C8
> H10
> H11
> C7
> H6
> H9
> o
> sy
> o
> n3
> hn
> hn
> ca
> ca
> ha
> ca
> ha
> ca
> ha
> ca
> ca
> c3
> hx
> hx
> n4
> hn
> hn
> c3
> hx
> hx
> c3
> hc
> hc
> -0.573668
> 1.232538
> -0.573668
> -1.037186
> 0.469850
> 0.469850
> -0.028732
> -0.216911
> 0.200250
> -0.129610
> 0.216974
> -0.225853
> 0.183828
> 0.053522
> 0.065648
> -0.178191
> 0.172836
> 0.172836
> -0.313324
> 0.348583
> 0.348583
> -0.090633
> 0.141132
> 0.141132
> 0.017190
> 0.066512
> 0.066512
>
>
>
> Dr. Fabian Glaser
> Head of the Structural Bioinformatics section
>
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
> Engineering Technion - Israel Institute of Technology, Haifa 32000,
> ISRAEL
>
> fglaser at technion dot ac dot il
> Tel: +972 4 8293701
> http://bku.technion.ac.il
>
>
> > On 25 Nov 2015, at 12:16 PM, Hannes Loeffler
> > <Hannes.Loeffler.stfc.ac.uk> wrote:
> >
> > Dear Fabian.
> >
> > if the authors have used GAFF you should be able to obtain the same
> > atoms types. Charges will of course vary depending on the
> > derivation method you use. Principally free energies are dependent
> > on force field parameters but I won't be able to tell you how much
> > that would be (there are a few papers out there which compare e.g.
> > GAFF to OPLS).
> >
> > A few points to check:
> > Reduce reads a dictionary of known PDB structures so make sure that
> > your PDB file does indeed name the ligand as SKF. Check reduce's
> > output to make sure that is true. Make sure that the hydrogens you
> > have obtained are the same as in the paper. If so you should get
> > the same atom types.
> >
> > The charge models used for the AMBER family of force fields is
> > basically RESP or AM1/BCC (there are some exceptions but look that
> > up in the manual).
> >
> > Cheers,
> > Hannes
> >
> >
> > On Wed, 25 Nov 2015 11:43:36 +0200
> > Fabian gmail <fabian.glaser.gmail.com> wrote:
> >
> >> Dear Hannes,
> >>
> >> I am trying to reproduce initially the results from the Kaus et al
> >> paper you mention for the first ligand
> >> ( 7-sulfamoyl-1,2,3,4-tetrahydroisoquinolinium), now if I am
> >> understand correctly first I need to obtain the mol2 file using
> >> antechamber with gaff model, starting from the PDB structure of
> >> this ligand this is what I tried to do using this commands:
> >>
> >> reduce SKF_A.pdb > SKF_hyd.pdb
> >> antechamber -i SKF_hyd.pdb -fi pdb -o SKF.mol2 -fo mol2 -c bcc -s 2
> >>
> >> This yields completely different atom types and charges as compared
> >> to the paper of Kaus, as expected since they used RESP model and I
> >> used AMB1-BCC, but I don’t have gaussian….
> >>
> >> Do you think the final DG value will be highly different using the
> >> bcc model or could you recommend to use a different model of those
> >> included in amber that I could use, which will provide more similar
> >> charges to the ones on the paper?
> >>
> >> Will those values highly impact the final results?
> >
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Received on Wed Nov 25 2015 - 03:30:03 PST
