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limmi

Member

Registered: 2023-11-23

Posts: 2

Missing reference parameter using HOMA

Dear Multiwfn community,

I am currently using Harmonic oscillator measure of aromaticity (HOMA) on a set of molecules and encountered "Missing reference parameter" errors, for some of the molecules. I suspect the problem is the utilization of ghost atoms. Here is one example output after starting the HOMA calculation:
"
Current reference bond length (Angstrom) and sigma parameters:
B -C :      1.4235    104.5070
B -N :      1.4020     72.0300
C -C :      1.3880    257.7000
C -N :      1.3340     93.5200
C -O :      1.2650    157.3800
C -P :      1.6980    118.9100
C -S :      1.6770     94.0900
N -N :      1.3090    130.3300
N -O :      1.2480     57.2100

Input indices of the atoms involved in the ring, e.g. 1,5,6,7,8,12
(Input q can return)
2, 1, 6, 7, 4, 3

         Atom pair         Contribution  Bond length(Angstrom)
    2(C )  --    1(O ):      -0.182123        1.348327
Error: Missing reference parameter for O -O
"

Best regards,

limmi

Last edited by limmi (2023-11-23 13:56:20)

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 2,011

Website

Re: Missing reference parameter using HOMA

Dear limmi,

Please upload your input file or send your input file to my E-mail, I can hardly answer this question without the input file for Multiwfn.

Best,

Tian

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 2,011

Website

Re: Missing reference parameter using HOMA

I have checked your .fch file, the atoms in the ring (according to bonding relationship) is 2,3,4,5,8,7, therefore you should input 2,3,4,5,8,7 in this interface, and result can be normally obtained.

        Atom pair         Contribution  Bond length(Angstrom)
   2(C )  --    3(N ):      -0.022401        1.371910
   3(N )  --    4(C ):      -0.064812        1.398484
   4(C )  --    5(N ):      -0.033910        1.380643
   5(N )  --    8(C ):      -0.109995        1.418006
   8(C )  --    7(C ):      -0.170641        1.451032
   7(C )  --    2(C ):      -0.037877        1.358303
HOMA value is    0.560364

limmi

Member

Registered: 2023-11-23

Posts: 2

Re: Missing reference parameter using HOMA

Thanks a lot for your answer!

I am a bit surprised, because the atomindices I used [2, 1, 6, 7, 4, 3] are correct according to rdkit for this molecule OC(NC(N1)=O)=CC1=O

However using the atom indices from the fchk [2,3,4,5,8,7] I am getting different atoms in rdkit:

Edit: I think i found the problem: Rdkit's numbering starts from 0, while the numbering for the .fchk files starts from 1.

Best regards,

limmi

Last edited by limmi (2023-11-24 14:06:56)