[phenixbb] Re: Error phenix refine with ligands

hello On Tue, Jan 7, 2025, 6:19 PM Miriam Cavinato wrote:

Hi Pavel,

actually someone already helped me and I managed to get my restraints correctly.

Thanks anyway, Miriam

Inviato da Outlook per Android https://aka.ms/AAb9ysg ------------------------------ *From:* Pavel Afonine *Sent:* Tuesday, January 7, 2025 6:13:36 PM *To:* Miriam Cavinato ; [email protected] *Subject:* Re: [phenixbb] Error phenix refine with ligands

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Hi Miriam,

could you please send me the model file directly? You mentioned it was attached, but I don't see any attachment. I’ll take care of this as soon as I have the file.

Best, Pavel

On 1/3/25 06:41, [email protected] wrote:

...

Hi everyone,

I am trying to refine my model containing a ligand (a thiophene -like molecule with a 7 carbon atom cycle attached). I create restraints with ready set utility or directly with eLBOW, then I use phenix.refine and I get this error: "fatal problems in interpreting model file: number of atoms with unknown nonbonded energy type symbols: 12 Please edit the model file to resolve the problems or/and supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definition if necessary". Another problem is that as soon as I try to open REEL or open any result to check restraints, Phenix crashes... I was wondering if someone has the same issue and can help me figure it out! Thanks in advance

Best regards Miriam _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

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