Dear all, I'm trying to refine my model bound with a ligand bearing a -SF5 moiety (-pentafluorosulfanyl). I have used openbabel/Grade web server or REEL to generate/edit the cif file for the ligand. I could obtain the desired octahedral geometry for the -SF5 group. However, both cases failed in real space refinement and I got the following error message: "Number of atoms with unknown nonbonded energy type symbols: 22337...". I would be very grateful if anyone can share experience about how to tackle this issue. Thanks in advance. Best wishes, Yung-Chieh Chen
Hi Yung-Chieh, this needs a closer look to know what's happening. Please send me files off list (model and all ligand cifs) and I will investigate. Pavel On 12/3/24 07:54, Yung-Chieh Chen wrote:
Dear all,
I'm trying to refine my model bound with a ligand bearing a -SF5 moiety (-pentafluorosulfanyl). I have used openbabel/Grade web server or REEL to generate/edit the cif file for the ligand. I could obtain the desired octahedral geometry for the -SF5 group. However, both cases failed in real space refinement and I got the following error message: "Number of atoms with unknown nonbonded energy type symbols: 22337...". I would be very grateful if anyone can share experience about how to tackle this issue. Thanks in advance.
Best wishes, Yung-Chieh Chen _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
hello
On Tue, Dec 3, 2024, 5:03 PM Pavel Afonine
Hi Yung-Chieh,
this needs a closer look to know what's happening. Please send me files off list (model and all ligand cifs) and I will investigate.
Pavel
On 12/3/24 07:54, Yung-Chieh Chen wrote:
Dear all,
I'm trying to refine my model bound with a ligand bearing a -SF5 moiety (-pentafluorosulfanyl). I have used openbabel/Grade web server or REEL to generate/edit the cif file for the ligand. I could obtain the desired octahedral geometry for the -SF5 group. However, both cases failed in real space refinement and I got the following error message: "Number of atoms with unknown nonbonded energy type symbols: 22337...". I would be very grateful if anyone can share experience about how to tackle this issue. Thanks in advance.
Best wishes, Yung-Chieh Chen _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
participants (3)
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Pavel Afonine -
Son Kenneth -
Yung-Chieh Chen