Posts by limmi

limmi · Multiwfn and wavefunction analysis

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

limmi · Multiwfn and wavefunction analysis

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

Multiwfn forum

#1Re:Multiwfn and wavefunction analysis»Missing reference parameter using HOMA»2023-11-24 12:36:33

#2Multiwfn and wavefunction analysis»Missing reference parameter using HOMA»2023-11-23 10:38:28

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