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 - 03:00:03 PST
